Remove sequence from fasta file by samtools
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
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Using samtools faidx with a large list of genomic loci
written by jsandler •
-
Fast way to extract specific sequences from large fasta
written by mnsp088 •
-
Samtools extraction output is empty
written by spidcock01 •
-
Problem with FASTA filtering
written by Janey •
-
Remove some IDs from IDs list
written by Janey •
-
Fasta file filtering
written by Janey •
-
Extract sequence from multifasta file using samtools
written by Lorraine Lebönk •
-
extract sequences from multi fasta using partial ID
written by dago
-
adit sequences ID
written by Kurban
-
Samtool (Faidx) - Signal 11 Termination Error
written by IsmailM
searching on this site would give you many solutions.
I searched this site but i didn't find suitable solution.
Does no one have any easy solution.
ID-list.txt: one ID per line.
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!
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