Hi guys!!!
I am terrible in unix scripting...but I have a feeling that is the only way to sort out my problem:
I want to filter out from my .gtf file from cufflinks those transcripts with a fpkm < 1.
I have tried
awk '($14>1)' transcripts.gtf > transcripts.b.gtf
but of course with no success...
$14 is the position of fpkm values
This is the first line of the .gtf file
1 Cufflinks transcript 53049 54936 1 + . gene_id "ENSG00000268020"; transcript_id "ENST00000594647"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; full_read_support "no";
Can anyone help???
thanks!
Manu
I am terrible in unix scripting...but I have a feeling that is the only way to sort out my problem:
I want to filter out from my .gtf file from cufflinks those transcripts with a fpkm < 1.
I have tried
awk '($14>1)' transcripts.gtf > transcripts.b.gtf
but of course with no success...
$14 is the position of fpkm values
This is the first line of the .gtf file
1 Cufflinks transcript 53049 54936 1 + . gene_id "ENSG00000268020"; transcript_id "ENST00000594647"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; full_read_support "no";
Can anyone help???
thanks!
Manu
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