Question: (Closed) Remove sequence from fasta file by samtools
0
gravatar for Janey
6 months ago by
Janey10
USA
Janey10 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 • 430 views
ADD COMMENTlink modified 6 months ago by RamRS19k • written 6 months ago by Janey10

searching on this site would give you many solutions.

ADD REPLYlink written 6 months ago by shenwei3564.3k

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

Does no one have any easy solution.

ADD REPLYlink written 6 months ago by Janey10
seqkit grep -v -f ID-list.txt seqs.fa

ID-list.txt: one ID per line.

ADD REPLYlink written 6 months ago by shenwei3564.3k

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 6 months ago by RamRS19k
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 6 months ago • written 6 months ago by finswimmer7.9k
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