Question: How to remove aligned sequnces?
gravatar for vishalchanda364
3 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 • 105 views
ADD COMMENTlink written 3 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 3 months ago by genomax83k

Thank You so much for the help.

ADD REPLYlink written 3 months ago by vishalchanda36420
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