Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Creating a mRNA GTF file from fasta for HTSeq ? CEPHSeq Bioinformatics 11 06-18-2015 09:44 AM
Problems creating GTF for Cufflinks annotation DrD2009 Bioinformatics 10 02-23-2015 06:20 AM
Creating "Consensus" Sequence between Reference and Mapped Reads roliwilhelm Genomic Resequencing 2 07-23-2012 11:21 AM
entamoeba histolytica reference genome (gene annotation file) in GTF format paula123 Bioinformatics 1 06-04-2012 02:39 AM
Extracting Reference Sequence from a bam File andy11 Bioinformatics 6 12-13-2010 02:06 PM

Thread Tools
Old 02-06-2013, 12:47 PM   #1
Location: Universe

Join Date: Dec 2012
Posts: 81
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.
syintel87 is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 10:16 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO