Question: (Closed) Remove sequence from fasta file by samtools
1
gravatar for Janey
2.5 years ago by
Janey30
USA
Janey30 wrote:

Hi

I use the following script to extract sequence from fasta file by samtools. How can I write similar command to remove the sequences by sequence IDs list from fasta file by samtools.

cut -c 2- ID.text | xargs -n 1 samtools faidx in.fasta > out.fasta

Thanks for your help

rna-seq • 3.0k views
ADD COMMENTlink modified 2.5 years ago by _r_am31k • written 2.5 years ago by Janey30

searching on this site would give you many solutions.

ADD REPLYlink written 2.5 years ago by shenwei3565.6k

I searched this site but i didn't find suitable solution.

Does no one have any easy solution.

ADD REPLYlink written 2.5 years ago by Janey30
seqkit grep -v -f ID-list.txt seqs.fa

ID-list.txt: one ID per line.

ADD REPLYlink written 2.5 years ago by shenwei3565.6k

Hello Janey!

We believe that this post does not fit the main topic of this site.

Please search the site - this is one of the most common questions here.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 2.5 years ago by _r_am31k
1

It is also a duplicate post from the same OP. Please stay in your original post and give reply to my question and the answers of the user users.

fin swimmer

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by finswimmer14k
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