Excluding or including by awk
2
$begingroup$
I have a gtf file as attached enter link description here
By this command one could extract coding parts of genome
awk '{if($3=="transcript" && $20==""protein_coding";"){print $0}}' gencode.gtf
How I could exclude coding parts from this file keeping non coding regions
linux wgs bash
asked 2 hours ago
Feresh TehFeresh Teh
38111
$endgroup$
add a comment |
2
$begingroup$
I have a gtf file as attached enter link description here
By this command one could extract coding parts of genome
awk '{if($3=="transcript" && $20==""protein_coding";"){print $0}}' gencode.gtf
How I could exclude coding parts from this file keeping non coding regions
linux wgs bash
asked 2 hours ago
Feresh TehFeresh Teh
38111
$endgroup$
add a comment |
2
2
2
1
$begingroup$
I have a gtf file as attached enter link description here
By this command one could extract coding parts of genome
awk '{if($3=="transcript" && $20==""protein_coding";"){print $0}}' gencode.gtf
How I could exclude coding parts from this file keeping non coding regions
linux wgs bash
asked 2 hours ago
Feresh TehFeresh Teh
38111
$endgroup$
I have a gtf file as attached enter link description here
By this command one could extract coding parts of genome
awk '{if($3=="transcript" && $20==""protein_coding";"){print $0}}' gencode.gtf
How I could exclude coding parts from this file keeping non coding regions
linux wgs bash
linux wgs bash
asked 2 hours ago
Feresh TehFeresh Teh
38111
asked 2 hours ago
Feresh TehFeresh Teh
38111
asked 2 hours ago
Feresh TehFeresh Teh
38111
asked 2 hours ago
Feresh TehFeresh Teh
38111
asked 2 hours ago
Feresh TehFeresh Teh
38111
38111
add a comment |
add a comment |
1 Answer
1
active
oldest
votes
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.
answered 1 hour ago
finswimmerfinswimmer
962210
$endgroup$
$begingroup$
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
1 hour ago
$begingroup$
Sorry I tried hat but my output is empty
$endgroup$
– Feresh Teh
1 hour 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
1 hour ago
$begingroup$
Thank you but both of your commands return nothing :(
$endgroup$
– Feresh Teh
1 hour ago
add a comment |
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1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
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.
answered 1 hour ago
finswimmerfinswimmer
962210
$endgroup$
$begingroup$
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
1 hour ago
$begingroup$
Sorry I tried hat but my output is empty
$endgroup$
– Feresh Teh
1 hour 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
1 hour ago
$begingroup$
Thank you but both of your commands return nothing :(
$endgroup$
– Feresh Teh
1 hour ago
add a comment |
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.
answered 1 hour ago
finswimmerfinswimmer
962210
$endgroup$
$begingroup$
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
1 hour ago
$begingroup$
Sorry I tried hat but my output is empty
$endgroup$
– Feresh Teh
1 hour 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
1 hour ago
$begingroup$
Thank you but both of your commands return nothing :(
$endgroup$
– Feresh Teh
1 hour ago
add a comment |
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.
answered 1 hour ago
finswimmerfinswimmer
962210
$endgroup$
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.
answered 1 hour ago
finswimmerfinswimmer
962210
edited 1 hour ago
answered 1 hour ago
finswimmerfinswimmer
962210
answered 1 hour ago
finswimmerfinswimmer
962210
answered 1 hour 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
1 hour ago
$begingroup$
Sorry I tried hat but my output is empty
$endgroup$
– Feresh Teh
1 hour 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
1 hour ago
$begingroup$
Thank you but both of your commands return nothing :(
$endgroup$
– Feresh Teh
1 hour ago
add a comment |
$begingroup$
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
1 hour ago
$begingroup$
Sorry I tried hat but my output is empty
$endgroup$
– Feresh Teh
1 hour 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
1 hour ago
$begingroup$
Thank you but both of your commands return nothing :(
$endgroup$
– Feresh Teh
1 hour 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
1 hour 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
1 hour ago
$begingroup$
Sorry I tried hat but my output is empty
$endgroup$
– Feresh Teh
1 hour ago
$begingroup$
Sorry I tried hat but my output is empty
$endgroup$
– Feresh Teh
1 hour 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
1 hour 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
1 hour ago
$begingroup$
Thank you but both of your commands return nothing :(
$endgroup$
– Feresh Teh
1 hour ago
$begingroup$
Thank you but both of your commands return nothing :(
$endgroup$
– Feresh Teh
1 hour ago
add a comment |
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