Question: fasta generation for functional elements
0
gravatar for ajmaninisha
4.4 years ago by
Canada
ajmaninisha0 wrote:

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 annoation 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

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by ajmaninisha0
0
gravatar for James Ashmore
4.4 years ago by
James Ashmore2.7k
UK/Edinburgh/MRC Centre for Regenerative Medicine
James Ashmore2.7k wrote:

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

ADD COMMENTlink written 4.4 years ago by James Ashmore2.7k
0
gravatar for ajmaninisha
4.4 years ago by
Canada
ajmaninisha0 wrote:

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

ADD COMMENTlink written 4.4 years ago by ajmaninisha0

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

ADD REPLYlink written 4.4 years ago by James Ashmore2.7k
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