Question: Retrieve only BLAST hit sequences from a de novo transcriptome
1
gravatar for Cristian Vergara
3.0 years ago by
Cristian Vergara20 wrote:

Hello!

I currently have a 255k assembled contigs transcriptome (de novo, Trinity) and I want to retrieve indentifiers and sequences in fasta format of the contigs that had hits in BLASTx (around 50%). There's any way to filter using the BLASTx output, an script and the transcriptome itself? O I should search an approach of parsing BLASTx output to contain sequences?.

Thanks in advance!

transcriptome rna-seq filter • 1.2k views
ADD COMMENTlink modified 3.0 years ago by natasha.sernova3.5k • written 3.0 years ago by Cristian Vergara20
3
gravatar for natasha.sernova
3.0 years ago by
natasha.sernova3.5k
natasha.sernova3.5k wrote:

Many people have encountered the problem before. See their ports:

How to deal with many uncharacterized protein in the blastx results?

Annotating sequences after de-novo Trinity assembly and RSEM analysis...there must be an easier way!

or this guide:

http://sfg.stanford.edu/BLAST.html

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by natasha.sernova3.5k
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