How to remove aligned sequnces?
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
• 977 views
•
link
written
by
vishalchanda364 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How to run BLAST locally for multiple fasta files
written by Paula •
-
Blast in parallel with edible outfmt
written by K.Gee •
-
Is building otu table in metagenomic analysis necessary?
written by vishalchanda364 •
-
Taking out the no hit sequences.
written by vishalchanda364 •
-
Family level taxonomic annotation
written by vishalchanda364 •
-
The number limitation of blast
written by horsedog •
-
Identify protein sequences from L.infantum with more than 60% conservancy with other Leishmania spe…
written by dzisis1986 •
-
do blast search using gi numbers
written by bitpir
-
Result difference between blastall -p blastp (legacy blast) and blastp -task blastp (blast+)
written by ahsan.chattha15 •
-
Problem with blastp when blasting against custom made database
written by thjnant
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
Thank You so much for the help.