Question: How to remove aligned sequnces?
gravatar for vishalchanda364
11 months ago by
vishalchanda36420 wrote:

Hello, I have been working on a metagenomic data, and now trying to remove ribosomal protein using the blastp command in BLAST+, I want to retain the sequences which doesn't map to the reference. Can anyone tell me how can I do that so that all the mapped sequences Bacterial gets removed and I am left with unmapped sequences which are possible Viral sequences.

The command I used for blastp is;

blastp -db cog -query ../../../Prodigal/F_V_0_29_R.faa -out ../../../blast/output_1 -evalue 1e-10

Thanks in advance, Vishal

sequencing next-gen alignment • 180 views
ADD COMMENTlink written 11 months ago by vishalchanda36420

Parse entries that don't have hits. You can then fish those sequences out of your file. Here are some options for that: Extract Sequence From Fasta File Using Ids From a separate txt File in linux

ADD REPLYlink written 11 months ago by GenoMax94k

Thank You so much for the help.

ADD REPLYlink written 11 months ago by vishalchanda36420
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1013 users visited in the last hour