How to extract Gene sequence from a fasta file using Cufflink ID?

Question

[AP]

Hello everyone,

I am trying to give function to differentially expressed genes across different samples. But now I have problem extracting fasta sequence for some differentially expressed genes.

I had a gtf file from augustus which I tried to merge it to gtf files generated by cufflink using cuffmerge. Now I realized that with some of the expressed genes I don't have gene name like g123, g6352, ect, but I have IDs like CUFF 2.1, CUFF 12.1, etc.

I already extracted fasta sequence from the genes having appropriate gene names. However I don't know how to extract sequence from other genes using cufflink IDs. Is there any solution to my problem. I will really appreciate your help.

Thank you,

Ambika

[Prasad]

Have you tried gffread or fastafrombed. Gffread has options to extract only coding region or proteins many more from gff/gtf

[AP]

No I haven't tried that. The problem is is my annotation file I don't have those cufflink Ids.

[cpad0112]

You can also use gtf_to_fasta (provided by tophat package, available in ubuntu repos), if you have gtf file..

Answer 1

[lakhujanivijay]

Do you have the locations for the sequences you want? If yes, then gffread is the answer