Question

Using awk to filter .gtf by FPKM

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3.9 years ago

ellenbdrake30 • 0

Hi,

I'm sorry if this is incredibly basic but I'm very new to working in terminal. I have a .gtf that I would like to filter based on an FPKM threshold. However, the column that contains FPKM values has these values in equations, so when I try with

awk '{if($16>0.3) print }' < file.gtf > new.file.gtf I get a blank file as output.

Is there a way around this? I've tried using quotations in my filtering step too, just in case awk '{if($16>"0.3") print but still get an empty file. Any tips would be greatly appreciated!!

RNA-Seq assembly • 1.5k views

ADD COMMENT • link 3.9 years ago by ellenbdrake30 • 0

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Hi, you will definitely need to show some sample input and desired output. Currently, we cannot see how your data is arranged.

ADD REPLY • link 3.9 years ago by Kevin Blighe 87k

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Thanks for letting me know Kevin!

ADD REPLY • link 3.9 years ago by ellenbdrake30 • 0

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Thanks for letting me know Kevin!

ADD REPLY • link 3.9 years ago by ellenbdrake30 • 0

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Here's an example of my data

chr1    StringTie   exon    3011039 3011386 1000    -   .   gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "1"; cov "2.586207";

chr1    StringTie   transcript  3026805 3027018 1000    -   .   gene_id "STRG.3"; transcript_id "STRG.3.1"; cov "2.803738"; FPKM "0.239292"; TPM "0.462935";

chr1    StringTie   exon    3026805 3027018 1000    -   .   gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "1"; cov "2.803738";

chr1    StringTie   transcript  3047584 3047862 1000    -   .   gene_id "STRG.4"; transcript_id "STRG.4.1"; cov "3.225806"; FPKM "0.275315"; TPM "0.532624";

chr1    StringTie   exon    3047584 3047862 1000    -   .   gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "1"; cov "3.225806";

chr1    StringTie   transcript  3057653 3057894 1000    +   .   gene_id "STRG.5"; transcript_id "STRG.5.1"; cov "2.789256"; FPKM "0.238056"; TPM "0.460544";

chr1    StringTie   exon    3057653 3057894 1000    +   .   gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "1"; cov "2.789256";

chr1    StringTie   transcript  3072676 3072886 1000    +   .   gene_id "STRG.6"; transcript_id "STRG.6.1"; cov "3.317536"; FPKM "0.283144"; TPM "0.547770";

chr1    StringTie   exon    3072676 3072886 1000    +   .   gene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "1"; cov "3.317536";

chr1    StringTie   transcript  3080222 3080714 1000    -   .   gene_id "STRG.7"; transcript_id "STRG.7.1"; cov "2.835700"; FPKM "0.242020"; TPM "0.468212";

ADD REPLY • link updated 3.9 years ago by Kevin Blighe 87k • written 3.9 years ago by ellenbdrake30 • 0

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If you just want an expression matrix, I would try Ballgown: A: Generating FPKM matrix accross all samples after stringtie

ADD REPLY • link 3.9 years ago by Kevin Blighe 87k

score 1 · Answer 1 · 2020-05-24

with input text (cut off is 0.25):

$ awk -F '"' '/FPKM/ { if ($8 > 0.25) print}' test.txt 
chr1    StringTie   transcript  3047584 3047862 1000    -   .   gene_id "STRG.4"; transcript_id "STRG.4.1"; cov "3.225806"; FPKM "0.275315"; TPM "0.532624";
chr1    StringTie   transcript  3072676 3072886 1000    +   .   gene_id "STRG.6"; transcript_id "STRG.6.1"; cov "3.317536"; FPKM "0.283144"; TPM "0.547770";