how to change gtf to fasta file of cufflink, gffread

Question

[worarado.kan]

Dear all,

I would like to change gtf file to fasta file. In gffread, if I need only TCONS_00033653 and gene_id "XLOC_028018 ID. what is command I should use?

My gtf file is

v.corymbosum_GDV_reftransV1_0039461 Cufflinks   exon    1171    1309    .-  .   gene_id "XLOC_028018"; transcript_id "TCONS_00033653"; exon_number "2"; oId "CUFF.29927.1"; tss_id "TSS29077";

Actually, I used gffread -w ECvsEL_transcript.fasta -g v.corymbosum_GDV_reftransV1.fasta EC_vs_EL.gtf

But I get only TCONS_00033653 ID

Thank you so much kanjana

[Sej Modha]

If I understand this, are you referring to FASTA file header when you mentioned

But I get only TCONS_00033653 ID

[worarado.kan]

Yes I mean head of fasta file because next step I have to joint fasta file with genes.exp.cuffdiff file, so I need the same ID

Could you help how to use command? sorry Im new for this analysis

Thank you so much Kanjana

Answer 1

[Kristoffer Vitting-Seerup]

For most genes you have quantified multiple transcripts. The expression of those transcripts have then been summed to get the gene expression - which is then used to o the gene differential expression. This also means that there is no single sequence which will represent the gene you have been analysing meaning it cannot be done.

What do you need the gene-sequence for? Maybe we can figure out an alternative approach if you tell us why you want to use it for :-)

Cheers Kristoffer