fasta generation for functional elements

Question

[ajmaninisha]

Hi,

I have got several suggestion how to extract fasta sequence from assembled cufflinks like to use gff read program or extract genomic DNA. Both of these programs help in generating fasta sequence with respect to the reference annotation file but I want to extract fasta sequence from mapped reads so that I have a better picture to find the functional elements present in my samples.This will also help to identify novel genes and transcripts.

Is there a better way to extract fasta format?

Thanks

NISHA

Answer 1

[James Ashmore]

I answered a question similar to this, please check my comment in this C: Tool to retrieve regions with reads?

Answer 2

[ajmaninisha]

Thanks james and is it possible to get fasta from assembled cufflinks transcript file too.

I am using galaxy so the tools suggested by you are available in the tool shed.

Thanks

[James Ashmore]

The bedtools getfasta command requires your query file to be in .bed format, so you could convert the transcript .gtf file into a .bed file and use that, again check the awk command I listed on the other thread to see how to do that, hope that helps