Identify non-coding regions from a genome annotation












4












$begingroup$


I have this GTF file and I use the command below on a Linux machine to extract the coding regions of the genome:



awk '{if($3=="transcript" && $20==""protein_coding";"){print $0}}' gencode.gtf


How I could do the inverse and keep only non coding regions?










share|improve this question











$endgroup$








  • 1




    $begingroup$
    Do you want all non-coding regions of the genome or do you want all non-coding transcripts? These are two very different things.
    $endgroup$
    – terdon
    10 hours ago
















4












$begingroup$


I have this GTF file and I use the command below on a Linux machine to extract the coding regions of the genome:



awk '{if($3=="transcript" && $20==""protein_coding";"){print $0}}' gencode.gtf


How I could do the inverse and keep only non coding regions?










share|improve this question











$endgroup$








  • 1




    $begingroup$
    Do you want all non-coding regions of the genome or do you want all non-coding transcripts? These are two very different things.
    $endgroup$
    – terdon
    10 hours ago














4












4








4


2



$begingroup$


I have this GTF file and I use the command below on a Linux machine to extract the coding regions of the genome:



awk '{if($3=="transcript" && $20==""protein_coding";"){print $0}}' gencode.gtf


How I could do the inverse and keep only non coding regions?










share|improve this question











$endgroup$




I have this GTF file and I use the command below on a Linux machine to extract the coding regions of the genome:



awk '{if($3=="transcript" && $20==""protein_coding";"){print $0}}' gencode.gtf


How I could do the inverse and keep only non coding regions?







annotation genome gtf text-processing interval






share|improve this question















share|improve this question













share|improve this question




share|improve this question








edited 10 hours ago









Daniel Standage

2,303329




2,303329










asked 16 hours ago









Feresh TehFeresh Teh

39311




39311








  • 1




    $begingroup$
    Do you want all non-coding regions of the genome or do you want all non-coding transcripts? These are two very different things.
    $endgroup$
    – terdon
    10 hours ago














  • 1




    $begingroup$
    Do you want all non-coding regions of the genome or do you want all non-coding transcripts? These are two very different things.
    $endgroup$
    – terdon
    10 hours ago








1




1




$begingroup$
Do you want all non-coding regions of the genome or do you want all non-coding transcripts? These are two very different things.
$endgroup$
– terdon
10 hours ago




$begingroup$
Do you want all non-coding regions of the genome or do you want all non-coding transcripts? These are two very different things.
$endgroup$
– terdon
10 hours ago










3 Answers
3






active

oldest

votes


















1












$begingroup$

If you want all transcripts from that gtf file whose type isn't "protein_coding", you can use almost the same command, just change the == ("is") to != ("isn't"):



awk '{if($3=="transcript" && $20!=""protein_coding";"){print $0}}' gencode.gtf 


Or, a simpler version:



awk '$3=="transcript" && $20!=""protein_coding";"' gencode.gtf 


Note that this will not include any of the havana transcripts in the file, but I am assuming that's what you want since that's what your original command did.



Specifically, the command will return the following types of transcript (the numbers on the left are the number of such transcripts in the file):



awk '$3=="transcript" && $20!=""protein_coding";"{print $20}' gencode.gtf  | sort | uniq -c | sort -nk1
1 "translated_processed_pseudogene";
2 "Mt_rRNA";
3 "IG_J_pseudogene";
3 "TR_D_gene";
4 "TR_J_pseudogene";
5 "TR_C_gene";
10 "IG_C_pseudogene";
18 "IG_C_gene";
18 "IG_J_gene";
22 "Mt_tRNA";
25 "3prime_overlapping_ncrna";
27 "TR_V_pseudogene";
37 "IG_D_gene";
58 "non_stop_decay";
59 "polymorphic_pseudogene";
74 "TR_J_gene";
97 "TR_V_gene";
144 "IG_V_gene";
182 "unitary_pseudogene";
196 "IG_V_pseudogene";
330 "sense_overlapping";
387 "pseudogene";
442 "transcribed_processed_pseudogene";
531 "rRNA";
802 "sense_intronic";
860 "transcribed_unprocessed_pseudogene";
1529 "snoRNA";
1923 "snRNA";
2050 "misc_RNA";
2549 "unprocessed_pseudogene";
3116 "miRNA";
9710 "antisense";
10623 "processed_pseudogene";
11780 "lincRNA";
13052 "nonsense_mediated_decay";
25955 "retained_intron";
28082 "processed_transcript";


You might also want to remove that "translated_processed_pseudogene" since that is actually translated into protein and is therefore technically coding:



awk '$3=="transcript" && 
$
20!=""protein_coding";" &&
$20!=""translated_processed_pseudogene";"' gencode.gtf





share|improve this answer











$endgroup$













  • $begingroup$
    Thanks a lot, really thank you for saving me I could not solve that myself. How I can extract the below information from each line of resulting non-coding file chr1 29553 30039 ENSG00000243485.2 + gene_name "MIR1302-11"
    $endgroup$
    – Feresh Teh
    8 hours ago












  • $begingroup$
    @FereshTeh you're welcome. I think you want awk '$3=="transcript" && $20!=""protein_coding";" && $20!=""translated_processed_pseudogene";"{print $1,$4,$5,$10,$7}' gencode.gtf but, if not, please ask a new question about that.
    $endgroup$
    – terdon
    8 hours ago










  • $begingroup$
    Thanks a lot that returns all except gene name, this is output chr1 29554 31097 "ENSG00000243485.2"; +
    $endgroup$
    – Feresh Teh
    8 hours ago






  • 1




    $begingroup$
    @FereshTeh please ask a new question so you can show exactly what output you need.
    $endgroup$
    – terdon
    8 hours ago



















3












$begingroup$

Getting the non coding regions of a protein coding transcript, sounds like you are looking for UTR.



UTR has its own feature in the gtf file. So you can do this:



$ awk -v FS="t" '$3=="UTR"' gencode.gtf


If the gtf file is compressed use this instead:



$ zcat gencode.gtf.gz | awk -v FS="t" '$3=="UTR"'


BTW: Why are you using such an old release of gencode? The current version is v29.






share|improve this answer











$endgroup$













  • $begingroup$
    Sorry, literally I need non coding regions of human genome, but for asking my question here I referred to coding parts too
    $endgroup$
    – Feresh Teh
    16 hours ago










  • $begingroup$
    Sorry I tried hat but my output is empty
    $endgroup$
    – Feresh Teh
    16 hours ago






  • 1




    $begingroup$
    As @Wouter tells you, the non coding region of a genome is the complement of the coding regions. Coding regions have its own feature in the gtf file. You can get them with $ awk -v FS="t" '$3=="CDS"' gencode.gtf. Reading the manual for bedtools complement is your task.
    $endgroup$
    – finswimmer
    16 hours ago












  • $begingroup$
    Sorry but your commands return nothing, I mean not working returning empty file
    $endgroup$
    – Feresh Teh
    10 hours ago










  • $begingroup$
    The gtf file the OP has linked to includes non-coding transcripts (LINCs, pseudogenes, tRNAs etc). I am guessing this is what they're after.
    $endgroup$
    – terdon
    10 hours ago



















2












$begingroup$

This isn't a problem that's easily solved with awk. It's not like you're extracting a feature that's annotated in the GTF file. Instead, you want the empty space between annotated features.



A few years ago I wrote a program called LocusPocus for a similar task. It uses a gene annotation to break down a genome into gene loci and intergenic regions. It handles overlapping annotations and other weirdness pretty robustly. The output will include both coding regions and non-coding regions, but you can identify the intergenic spaces as those with iLocus_type equal to iiLocus or fiLocus.



Note: the --delta parameter will extend each gene/transcript by 500bp by default.



Caveat: the program only accepts GFF3 input by default. Hopefully it won't be too hard to convert your GTF to GFF3.



Another caveat: eventual interpretation of these data will depend on what features are annotated in the genome and which annotations you include vs ignore. Do you want your non-coding regions to include non-coding genes, or should these be treated separately? Some non-coding regions will be full of transposable elements and other repetitive DNA, while others will have enhancers, promoters, or other regulatory elements. It's important to tread carefully before you jump to any conclusions.






share|improve this answer











$endgroup$









  • 1




    $begingroup$
    Absolutely brilliant name! :)
    $endgroup$
    – terdon
    9 hours ago











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3 Answers
3






active

oldest

votes








3 Answers
3






active

oldest

votes









active

oldest

votes






active

oldest

votes









1












$begingroup$

If you want all transcripts from that gtf file whose type isn't "protein_coding", you can use almost the same command, just change the == ("is") to != ("isn't"):



awk '{if($3=="transcript" && $20!=""protein_coding";"){print $0}}' gencode.gtf 


Or, a simpler version:



awk '$3=="transcript" && $20!=""protein_coding";"' gencode.gtf 


Note that this will not include any of the havana transcripts in the file, but I am assuming that's what you want since that's what your original command did.



Specifically, the command will return the following types of transcript (the numbers on the left are the number of such transcripts in the file):



awk '$3=="transcript" && $20!=""protein_coding";"{print $20}' gencode.gtf  | sort | uniq -c | sort -nk1
1 "translated_processed_pseudogene";
2 "Mt_rRNA";
3 "IG_J_pseudogene";
3 "TR_D_gene";
4 "TR_J_pseudogene";
5 "TR_C_gene";
10 "IG_C_pseudogene";
18 "IG_C_gene";
18 "IG_J_gene";
22 "Mt_tRNA";
25 "3prime_overlapping_ncrna";
27 "TR_V_pseudogene";
37 "IG_D_gene";
58 "non_stop_decay";
59 "polymorphic_pseudogene";
74 "TR_J_gene";
97 "TR_V_gene";
144 "IG_V_gene";
182 "unitary_pseudogene";
196 "IG_V_pseudogene";
330 "sense_overlapping";
387 "pseudogene";
442 "transcribed_processed_pseudogene";
531 "rRNA";
802 "sense_intronic";
860 "transcribed_unprocessed_pseudogene";
1529 "snoRNA";
1923 "snRNA";
2050 "misc_RNA";
2549 "unprocessed_pseudogene";
3116 "miRNA";
9710 "antisense";
10623 "processed_pseudogene";
11780 "lincRNA";
13052 "nonsense_mediated_decay";
25955 "retained_intron";
28082 "processed_transcript";


You might also want to remove that "translated_processed_pseudogene" since that is actually translated into protein and is therefore technically coding:



awk '$3=="transcript" && 
$
20!=""protein_coding";" &&
$20!=""translated_processed_pseudogene";"' gencode.gtf





share|improve this answer











$endgroup$













  • $begingroup$
    Thanks a lot, really thank you for saving me I could not solve that myself. How I can extract the below information from each line of resulting non-coding file chr1 29553 30039 ENSG00000243485.2 + gene_name "MIR1302-11"
    $endgroup$
    – Feresh Teh
    8 hours ago












  • $begingroup$
    @FereshTeh you're welcome. I think you want awk '$3=="transcript" && $20!=""protein_coding";" && $20!=""translated_processed_pseudogene";"{print $1,$4,$5,$10,$7}' gencode.gtf but, if not, please ask a new question about that.
    $endgroup$
    – terdon
    8 hours ago










  • $begingroup$
    Thanks a lot that returns all except gene name, this is output chr1 29554 31097 "ENSG00000243485.2"; +
    $endgroup$
    – Feresh Teh
    8 hours ago






  • 1




    $begingroup$
    @FereshTeh please ask a new question so you can show exactly what output you need.
    $endgroup$
    – terdon
    8 hours ago
















1












$begingroup$

If you want all transcripts from that gtf file whose type isn't "protein_coding", you can use almost the same command, just change the == ("is") to != ("isn't"):



awk '{if($3=="transcript" && $20!=""protein_coding";"){print $0}}' gencode.gtf 


Or, a simpler version:



awk '$3=="transcript" && $20!=""protein_coding";"' gencode.gtf 


Note that this will not include any of the havana transcripts in the file, but I am assuming that's what you want since that's what your original command did.



Specifically, the command will return the following types of transcript (the numbers on the left are the number of such transcripts in the file):



awk '$3=="transcript" && $20!=""protein_coding";"{print $20}' gencode.gtf  | sort | uniq -c | sort -nk1
1 "translated_processed_pseudogene";
2 "Mt_rRNA";
3 "IG_J_pseudogene";
3 "TR_D_gene";
4 "TR_J_pseudogene";
5 "TR_C_gene";
10 "IG_C_pseudogene";
18 "IG_C_gene";
18 "IG_J_gene";
22 "Mt_tRNA";
25 "3prime_overlapping_ncrna";
27 "TR_V_pseudogene";
37 "IG_D_gene";
58 "non_stop_decay";
59 "polymorphic_pseudogene";
74 "TR_J_gene";
97 "TR_V_gene";
144 "IG_V_gene";
182 "unitary_pseudogene";
196 "IG_V_pseudogene";
330 "sense_overlapping";
387 "pseudogene";
442 "transcribed_processed_pseudogene";
531 "rRNA";
802 "sense_intronic";
860 "transcribed_unprocessed_pseudogene";
1529 "snoRNA";
1923 "snRNA";
2050 "misc_RNA";
2549 "unprocessed_pseudogene";
3116 "miRNA";
9710 "antisense";
10623 "processed_pseudogene";
11780 "lincRNA";
13052 "nonsense_mediated_decay";
25955 "retained_intron";
28082 "processed_transcript";


You might also want to remove that "translated_processed_pseudogene" since that is actually translated into protein and is therefore technically coding:



awk '$3=="transcript" && 
$
20!=""protein_coding";" &&
$20!=""translated_processed_pseudogene";"' gencode.gtf





share|improve this answer











$endgroup$













  • $begingroup$
    Thanks a lot, really thank you for saving me I could not solve that myself. How I can extract the below information from each line of resulting non-coding file chr1 29553 30039 ENSG00000243485.2 + gene_name "MIR1302-11"
    $endgroup$
    – Feresh Teh
    8 hours ago












  • $begingroup$
    @FereshTeh you're welcome. I think you want awk '$3=="transcript" && $20!=""protein_coding";" && $20!=""translated_processed_pseudogene";"{print $1,$4,$5,$10,$7}' gencode.gtf but, if not, please ask a new question about that.
    $endgroup$
    – terdon
    8 hours ago










  • $begingroup$
    Thanks a lot that returns all except gene name, this is output chr1 29554 31097 "ENSG00000243485.2"; +
    $endgroup$
    – Feresh Teh
    8 hours ago






  • 1




    $begingroup$
    @FereshTeh please ask a new question so you can show exactly what output you need.
    $endgroup$
    – terdon
    8 hours ago














1












1








1





$begingroup$

If you want all transcripts from that gtf file whose type isn't "protein_coding", you can use almost the same command, just change the == ("is") to != ("isn't"):



awk '{if($3=="transcript" && $20!=""protein_coding";"){print $0}}' gencode.gtf 


Or, a simpler version:



awk '$3=="transcript" && $20!=""protein_coding";"' gencode.gtf 


Note that this will not include any of the havana transcripts in the file, but I am assuming that's what you want since that's what your original command did.



Specifically, the command will return the following types of transcript (the numbers on the left are the number of such transcripts in the file):



awk '$3=="transcript" && $20!=""protein_coding";"{print $20}' gencode.gtf  | sort | uniq -c | sort -nk1
1 "translated_processed_pseudogene";
2 "Mt_rRNA";
3 "IG_J_pseudogene";
3 "TR_D_gene";
4 "TR_J_pseudogene";
5 "TR_C_gene";
10 "IG_C_pseudogene";
18 "IG_C_gene";
18 "IG_J_gene";
22 "Mt_tRNA";
25 "3prime_overlapping_ncrna";
27 "TR_V_pseudogene";
37 "IG_D_gene";
58 "non_stop_decay";
59 "polymorphic_pseudogene";
74 "TR_J_gene";
97 "TR_V_gene";
144 "IG_V_gene";
182 "unitary_pseudogene";
196 "IG_V_pseudogene";
330 "sense_overlapping";
387 "pseudogene";
442 "transcribed_processed_pseudogene";
531 "rRNA";
802 "sense_intronic";
860 "transcribed_unprocessed_pseudogene";
1529 "snoRNA";
1923 "snRNA";
2050 "misc_RNA";
2549 "unprocessed_pseudogene";
3116 "miRNA";
9710 "antisense";
10623 "processed_pseudogene";
11780 "lincRNA";
13052 "nonsense_mediated_decay";
25955 "retained_intron";
28082 "processed_transcript";


You might also want to remove that "translated_processed_pseudogene" since that is actually translated into protein and is therefore technically coding:



awk '$3=="transcript" && 
$
20!=""protein_coding";" &&
$20!=""translated_processed_pseudogene";"' gencode.gtf





share|improve this answer











$endgroup$



If you want all transcripts from that gtf file whose type isn't "protein_coding", you can use almost the same command, just change the == ("is") to != ("isn't"):



awk '{if($3=="transcript" && $20!=""protein_coding";"){print $0}}' gencode.gtf 


Or, a simpler version:



awk '$3=="transcript" && $20!=""protein_coding";"' gencode.gtf 


Note that this will not include any of the havana transcripts in the file, but I am assuming that's what you want since that's what your original command did.



Specifically, the command will return the following types of transcript (the numbers on the left are the number of such transcripts in the file):



awk '$3=="transcript" && $20!=""protein_coding";"{print $20}' gencode.gtf  | sort | uniq -c | sort -nk1
1 "translated_processed_pseudogene";
2 "Mt_rRNA";
3 "IG_J_pseudogene";
3 "TR_D_gene";
4 "TR_J_pseudogene";
5 "TR_C_gene";
10 "IG_C_pseudogene";
18 "IG_C_gene";
18 "IG_J_gene";
22 "Mt_tRNA";
25 "3prime_overlapping_ncrna";
27 "TR_V_pseudogene";
37 "IG_D_gene";
58 "non_stop_decay";
59 "polymorphic_pseudogene";
74 "TR_J_gene";
97 "TR_V_gene";
144 "IG_V_gene";
182 "unitary_pseudogene";
196 "IG_V_pseudogene";
330 "sense_overlapping";
387 "pseudogene";
442 "transcribed_processed_pseudogene";
531 "rRNA";
802 "sense_intronic";
860 "transcribed_unprocessed_pseudogene";
1529 "snoRNA";
1923 "snRNA";
2050 "misc_RNA";
2549 "unprocessed_pseudogene";
3116 "miRNA";
9710 "antisense";
10623 "processed_pseudogene";
11780 "lincRNA";
13052 "nonsense_mediated_decay";
25955 "retained_intron";
28082 "processed_transcript";


You might also want to remove that "translated_processed_pseudogene" since that is actually translated into protein and is therefore technically coding:



awk '$3=="transcript" && 
$
20!=""protein_coding";" &&
$20!=""translated_processed_pseudogene";"' gencode.gtf






share|improve this answer














share|improve this answer



share|improve this answer








edited 8 hours ago

























answered 10 hours ago









terdonterdon

4,2841729




4,2841729












  • $begingroup$
    Thanks a lot, really thank you for saving me I could not solve that myself. How I can extract the below information from each line of resulting non-coding file chr1 29553 30039 ENSG00000243485.2 + gene_name "MIR1302-11"
    $endgroup$
    – Feresh Teh
    8 hours ago












  • $begingroup$
    @FereshTeh you're welcome. I think you want awk '$3=="transcript" && $20!=""protein_coding";" && $20!=""translated_processed_pseudogene";"{print $1,$4,$5,$10,$7}' gencode.gtf but, if not, please ask a new question about that.
    $endgroup$
    – terdon
    8 hours ago










  • $begingroup$
    Thanks a lot that returns all except gene name, this is output chr1 29554 31097 "ENSG00000243485.2"; +
    $endgroup$
    – Feresh Teh
    8 hours ago






  • 1




    $begingroup$
    @FereshTeh please ask a new question so you can show exactly what output you need.
    $endgroup$
    – terdon
    8 hours ago


















  • $begingroup$
    Thanks a lot, really thank you for saving me I could not solve that myself. How I can extract the below information from each line of resulting non-coding file chr1 29553 30039 ENSG00000243485.2 + gene_name "MIR1302-11"
    $endgroup$
    – Feresh Teh
    8 hours ago












  • $begingroup$
    @FereshTeh you're welcome. I think you want awk '$3=="transcript" && $20!=""protein_coding";" && $20!=""translated_processed_pseudogene";"{print $1,$4,$5,$10,$7}' gencode.gtf but, if not, please ask a new question about that.
    $endgroup$
    – terdon
    8 hours ago










  • $begingroup$
    Thanks a lot that returns all except gene name, this is output chr1 29554 31097 "ENSG00000243485.2"; +
    $endgroup$
    – Feresh Teh
    8 hours ago






  • 1




    $begingroup$
    @FereshTeh please ask a new question so you can show exactly what output you need.
    $endgroup$
    – terdon
    8 hours ago
















$begingroup$
Thanks a lot, really thank you for saving me I could not solve that myself. How I can extract the below information from each line of resulting non-coding file chr1 29553 30039 ENSG00000243485.2 + gene_name "MIR1302-11"
$endgroup$
– Feresh Teh
8 hours ago






$begingroup$
Thanks a lot, really thank you for saving me I could not solve that myself. How I can extract the below information from each line of resulting non-coding file chr1 29553 30039 ENSG00000243485.2 + gene_name "MIR1302-11"
$endgroup$
– Feresh Teh
8 hours ago














$begingroup$
@FereshTeh you're welcome. I think you want awk '$3=="transcript" && $20!=""protein_coding";" && $20!=""translated_processed_pseudogene";"{print $1,$4,$5,$10,$7}' gencode.gtf but, if not, please ask a new question about that.
$endgroup$
– terdon
8 hours ago




$begingroup$
@FereshTeh you're welcome. I think you want awk '$3=="transcript" && $20!=""protein_coding";" && $20!=""translated_processed_pseudogene";"{print $1,$4,$5,$10,$7}' gencode.gtf but, if not, please ask a new question about that.
$endgroup$
– terdon
8 hours ago












$begingroup$
Thanks a lot that returns all except gene name, this is output chr1 29554 31097 "ENSG00000243485.2"; +
$endgroup$
– Feresh Teh
8 hours ago




$begingroup$
Thanks a lot that returns all except gene name, this is output chr1 29554 31097 "ENSG00000243485.2"; +
$endgroup$
– Feresh Teh
8 hours ago




1




1




$begingroup$
@FereshTeh please ask a new question so you can show exactly what output you need.
$endgroup$
– terdon
8 hours ago




$begingroup$
@FereshTeh please ask a new question so you can show exactly what output you need.
$endgroup$
– terdon
8 hours ago











3












$begingroup$

Getting the non coding regions of a protein coding transcript, sounds like you are looking for UTR.



UTR has its own feature in the gtf file. So you can do this:



$ awk -v FS="t" '$3=="UTR"' gencode.gtf


If the gtf file is compressed use this instead:



$ zcat gencode.gtf.gz | awk -v FS="t" '$3=="UTR"'


BTW: Why are you using such an old release of gencode? The current version is v29.






share|improve this answer











$endgroup$













  • $begingroup$
    Sorry, literally I need non coding regions of human genome, but for asking my question here I referred to coding parts too
    $endgroup$
    – Feresh Teh
    16 hours ago










  • $begingroup$
    Sorry I tried hat but my output is empty
    $endgroup$
    – Feresh Teh
    16 hours ago






  • 1




    $begingroup$
    As @Wouter tells you, the non coding region of a genome is the complement of the coding regions. Coding regions have its own feature in the gtf file. You can get them with $ awk -v FS="t" '$3=="CDS"' gencode.gtf. Reading the manual for bedtools complement is your task.
    $endgroup$
    – finswimmer
    16 hours ago












  • $begingroup$
    Sorry but your commands return nothing, I mean not working returning empty file
    $endgroup$
    – Feresh Teh
    10 hours ago










  • $begingroup$
    The gtf file the OP has linked to includes non-coding transcripts (LINCs, pseudogenes, tRNAs etc). I am guessing this is what they're after.
    $endgroup$
    – terdon
    10 hours ago
















3












$begingroup$

Getting the non coding regions of a protein coding transcript, sounds like you are looking for UTR.



UTR has its own feature in the gtf file. So you can do this:



$ awk -v FS="t" '$3=="UTR"' gencode.gtf


If the gtf file is compressed use this instead:



$ zcat gencode.gtf.gz | awk -v FS="t" '$3=="UTR"'


BTW: Why are you using such an old release of gencode? The current version is v29.






share|improve this answer











$endgroup$













  • $begingroup$
    Sorry, literally I need non coding regions of human genome, but for asking my question here I referred to coding parts too
    $endgroup$
    – Feresh Teh
    16 hours ago










  • $begingroup$
    Sorry I tried hat but my output is empty
    $endgroup$
    – Feresh Teh
    16 hours ago






  • 1




    $begingroup$
    As @Wouter tells you, the non coding region of a genome is the complement of the coding regions. Coding regions have its own feature in the gtf file. You can get them with $ awk -v FS="t" '$3=="CDS"' gencode.gtf. Reading the manual for bedtools complement is your task.
    $endgroup$
    – finswimmer
    16 hours ago












  • $begingroup$
    Sorry but your commands return nothing, I mean not working returning empty file
    $endgroup$
    – Feresh Teh
    10 hours ago










  • $begingroup$
    The gtf file the OP has linked to includes non-coding transcripts (LINCs, pseudogenes, tRNAs etc). I am guessing this is what they're after.
    $endgroup$
    – terdon
    10 hours ago














3












3








3





$begingroup$

Getting the non coding regions of a protein coding transcript, sounds like you are looking for UTR.



UTR has its own feature in the gtf file. So you can do this:



$ awk -v FS="t" '$3=="UTR"' gencode.gtf


If the gtf file is compressed use this instead:



$ zcat gencode.gtf.gz | awk -v FS="t" '$3=="UTR"'


BTW: Why are you using such an old release of gencode? The current version is v29.






share|improve this answer











$endgroup$



Getting the non coding regions of a protein coding transcript, sounds like you are looking for UTR.



UTR has its own feature in the gtf file. So you can do this:



$ awk -v FS="t" '$3=="UTR"' gencode.gtf


If the gtf file is compressed use this instead:



$ zcat gencode.gtf.gz | awk -v FS="t" '$3=="UTR"'


BTW: Why are you using such an old release of gencode? The current version is v29.







share|improve this answer














share|improve this answer



share|improve this answer








edited 16 hours ago

























answered 16 hours ago









finswimmerfinswimmer

962210




962210












  • $begingroup$
    Sorry, literally I need non coding regions of human genome, but for asking my question here I referred to coding parts too
    $endgroup$
    – Feresh Teh
    16 hours ago










  • $begingroup$
    Sorry I tried hat but my output is empty
    $endgroup$
    – Feresh Teh
    16 hours ago






  • 1




    $begingroup$
    As @Wouter tells you, the non coding region of a genome is the complement of the coding regions. Coding regions have its own feature in the gtf file. You can get them with $ awk -v FS="t" '$3=="CDS"' gencode.gtf. Reading the manual for bedtools complement is your task.
    $endgroup$
    – finswimmer
    16 hours ago












  • $begingroup$
    Sorry but your commands return nothing, I mean not working returning empty file
    $endgroup$
    – Feresh Teh
    10 hours ago










  • $begingroup$
    The gtf file the OP has linked to includes non-coding transcripts (LINCs, pseudogenes, tRNAs etc). I am guessing this is what they're after.
    $endgroup$
    – terdon
    10 hours ago


















  • $begingroup$
    Sorry, literally I need non coding regions of human genome, but for asking my question here I referred to coding parts too
    $endgroup$
    – Feresh Teh
    16 hours ago










  • $begingroup$
    Sorry I tried hat but my output is empty
    $endgroup$
    – Feresh Teh
    16 hours ago






  • 1




    $begingroup$
    As @Wouter tells you, the non coding region of a genome is the complement of the coding regions. Coding regions have its own feature in the gtf file. You can get them with $ awk -v FS="t" '$3=="CDS"' gencode.gtf. Reading the manual for bedtools complement is your task.
    $endgroup$
    – finswimmer
    16 hours ago












  • $begingroup$
    Sorry but your commands return nothing, I mean not working returning empty file
    $endgroup$
    – Feresh Teh
    10 hours ago










  • $begingroup$
    The gtf file the OP has linked to includes non-coding transcripts (LINCs, pseudogenes, tRNAs etc). I am guessing this is what they're after.
    $endgroup$
    – terdon
    10 hours ago
















$begingroup$
Sorry, literally I need non coding regions of human genome, but for asking my question here I referred to coding parts too
$endgroup$
– Feresh Teh
16 hours ago




$begingroup$
Sorry, literally I need non coding regions of human genome, but for asking my question here I referred to coding parts too
$endgroup$
– Feresh Teh
16 hours ago












$begingroup$
Sorry I tried hat but my output is empty
$endgroup$
– Feresh Teh
16 hours ago




$begingroup$
Sorry I tried hat but my output is empty
$endgroup$
– Feresh Teh
16 hours ago




1




1




$begingroup$
As @Wouter tells you, the non coding region of a genome is the complement of the coding regions. Coding regions have its own feature in the gtf file. You can get them with $ awk -v FS="t" '$3=="CDS"' gencode.gtf. Reading the manual for bedtools complement is your task.
$endgroup$
– finswimmer
16 hours ago






$begingroup$
As @Wouter tells you, the non coding region of a genome is the complement of the coding regions. Coding regions have its own feature in the gtf file. You can get them with $ awk -v FS="t" '$3=="CDS"' gencode.gtf. Reading the manual for bedtools complement is your task.
$endgroup$
– finswimmer
16 hours ago














$begingroup$
Sorry but your commands return nothing, I mean not working returning empty file
$endgroup$
– Feresh Teh
10 hours ago




$begingroup$
Sorry but your commands return nothing, I mean not working returning empty file
$endgroup$
– Feresh Teh
10 hours ago












$begingroup$
The gtf file the OP has linked to includes non-coding transcripts (LINCs, pseudogenes, tRNAs etc). I am guessing this is what they're after.
$endgroup$
– terdon
10 hours ago




$begingroup$
The gtf file the OP has linked to includes non-coding transcripts (LINCs, pseudogenes, tRNAs etc). I am guessing this is what they're after.
$endgroup$
– terdon
10 hours ago











2












$begingroup$

This isn't a problem that's easily solved with awk. It's not like you're extracting a feature that's annotated in the GTF file. Instead, you want the empty space between annotated features.



A few years ago I wrote a program called LocusPocus for a similar task. It uses a gene annotation to break down a genome into gene loci and intergenic regions. It handles overlapping annotations and other weirdness pretty robustly. The output will include both coding regions and non-coding regions, but you can identify the intergenic spaces as those with iLocus_type equal to iiLocus or fiLocus.



Note: the --delta parameter will extend each gene/transcript by 500bp by default.



Caveat: the program only accepts GFF3 input by default. Hopefully it won't be too hard to convert your GTF to GFF3.



Another caveat: eventual interpretation of these data will depend on what features are annotated in the genome and which annotations you include vs ignore. Do you want your non-coding regions to include non-coding genes, or should these be treated separately? Some non-coding regions will be full of transposable elements and other repetitive DNA, while others will have enhancers, promoters, or other regulatory elements. It's important to tread carefully before you jump to any conclusions.






share|improve this answer











$endgroup$









  • 1




    $begingroup$
    Absolutely brilliant name! :)
    $endgroup$
    – terdon
    9 hours ago
















2












$begingroup$

This isn't a problem that's easily solved with awk. It's not like you're extracting a feature that's annotated in the GTF file. Instead, you want the empty space between annotated features.



A few years ago I wrote a program called LocusPocus for a similar task. It uses a gene annotation to break down a genome into gene loci and intergenic regions. It handles overlapping annotations and other weirdness pretty robustly. The output will include both coding regions and non-coding regions, but you can identify the intergenic spaces as those with iLocus_type equal to iiLocus or fiLocus.



Note: the --delta parameter will extend each gene/transcript by 500bp by default.



Caveat: the program only accepts GFF3 input by default. Hopefully it won't be too hard to convert your GTF to GFF3.



Another caveat: eventual interpretation of these data will depend on what features are annotated in the genome and which annotations you include vs ignore. Do you want your non-coding regions to include non-coding genes, or should these be treated separately? Some non-coding regions will be full of transposable elements and other repetitive DNA, while others will have enhancers, promoters, or other regulatory elements. It's important to tread carefully before you jump to any conclusions.






share|improve this answer











$endgroup$









  • 1




    $begingroup$
    Absolutely brilliant name! :)
    $endgroup$
    – terdon
    9 hours ago














2












2








2





$begingroup$

This isn't a problem that's easily solved with awk. It's not like you're extracting a feature that's annotated in the GTF file. Instead, you want the empty space between annotated features.



A few years ago I wrote a program called LocusPocus for a similar task. It uses a gene annotation to break down a genome into gene loci and intergenic regions. It handles overlapping annotations and other weirdness pretty robustly. The output will include both coding regions and non-coding regions, but you can identify the intergenic spaces as those with iLocus_type equal to iiLocus or fiLocus.



Note: the --delta parameter will extend each gene/transcript by 500bp by default.



Caveat: the program only accepts GFF3 input by default. Hopefully it won't be too hard to convert your GTF to GFF3.



Another caveat: eventual interpretation of these data will depend on what features are annotated in the genome and which annotations you include vs ignore. Do you want your non-coding regions to include non-coding genes, or should these be treated separately? Some non-coding regions will be full of transposable elements and other repetitive DNA, while others will have enhancers, promoters, or other regulatory elements. It's important to tread carefully before you jump to any conclusions.






share|improve this answer











$endgroup$



This isn't a problem that's easily solved with awk. It's not like you're extracting a feature that's annotated in the GTF file. Instead, you want the empty space between annotated features.



A few years ago I wrote a program called LocusPocus for a similar task. It uses a gene annotation to break down a genome into gene loci and intergenic regions. It handles overlapping annotations and other weirdness pretty robustly. The output will include both coding regions and non-coding regions, but you can identify the intergenic spaces as those with iLocus_type equal to iiLocus or fiLocus.



Note: the --delta parameter will extend each gene/transcript by 500bp by default.



Caveat: the program only accepts GFF3 input by default. Hopefully it won't be too hard to convert your GTF to GFF3.



Another caveat: eventual interpretation of these data will depend on what features are annotated in the genome and which annotations you include vs ignore. Do you want your non-coding regions to include non-coding genes, or should these be treated separately? Some non-coding regions will be full of transposable elements and other repetitive DNA, while others will have enhancers, promoters, or other regulatory elements. It's important to tread carefully before you jump to any conclusions.







share|improve this answer














share|improve this answer



share|improve this answer








edited 10 hours ago

























answered 10 hours ago









Daniel StandageDaniel Standage

2,303329




2,303329








  • 1




    $begingroup$
    Absolutely brilliant name! :)
    $endgroup$
    – terdon
    9 hours ago














  • 1




    $begingroup$
    Absolutely brilliant name! :)
    $endgroup$
    – terdon
    9 hours ago








1




1




$begingroup$
Absolutely brilliant name! :)
$endgroup$
– terdon
9 hours ago




$begingroup$
Absolutely brilliant name! :)
$endgroup$
– terdon
9 hours ago


















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