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Old 02-06-2013, 12:47 PM   #1
syintel87
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Default Creating new FA by extracting particular annotation (GTF) and sequence (reference FA)

I've got some list of differentially expressed genes.
Then, as a next step, I want to do blast.

Before doing blast, I want to make a new fasta file.
Regarding the genes that are identified as differentially expressed,
I would like to extract the position of those genes from annotation.gtf,
and, based on this position, extract the sequence from reference.fasta.

Then, with this new fasta file, I want to do blast.
Would you recommend some way to do this? Is there a software which has this function other than galaxy or gffread?

Thank you in advance.

Last edited by syintel87; 02-06-2013 at 01:57 PM.
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