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empty output of cds.fa from gffread

Hello,

I am using gffread (v0.12.7) to extract transcript sequences based on a stringtie merged gtf file. After looking through gffread's usage, I want to use -w to extract sequences of exons, and -x to extract cds.

My command are as following:

gffread -w exon.fa -x cds.fa -g genome stringtie_merged.gtf

The result exon.fa seems fine, but cds.fa is an empty file. I am wondering is there anything I can do about this.

Thanks a lot, Liyong

seq extract cds gffread transcript
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written by liyong • liyong

Hi! Does your GTF have annotation of CDS's?

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written by iraun iraun

Hello,

I just checked the GTF, it doesn't have any CDS. Thank you very much for pointing this out.
I might need to figure out how to add this feature to stringtie merge result.

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written by liyong • liyong

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