Extract sequences from a FASTA file using a gtf file

Question

[sdbaney]

Hi, I have a de novo assembled FASTA file that I used with Cuffdiff. I now have a sorted gtf file (only retained the transcripts that were significantly differentially expressed).

Is there a program that I can use to: 1. pull only the transcripts listed in the gtf file from the FASTA file 2. find the longest ORFs

so that I can run some manual BLAST searches to validate my semi-automatic BLAST.

Is there an easy way to do this? Perhaps I just need to run a search function in the FASTA file using the transcript IDs listed in my sorted gtf file.

Answer 1

[WouterDeCoster]

The first part looks like a job for bedtools getfasta.

[swbarnes2]

Duh duh duh duh duh duh doo doo doo da! BEDTools!

[WouterDeCoster]

Most bioinformaticians to be replaced by BEDTools

[Carlo Yague]

Love the comments xD

[swbarnes2]

Dun dun DUNNNNNNNNN!

Answer 2

[Carlo Yague]

1. Pull only the transcripts listed in the gtf file from the FASTA file

Use bedtools getfasta.

1. Find the longest ORFs

See this related thread for some options.