problem of using subseq

[ymwur]

Hi,
I try to extract sequences from a fastq file using the "subseq" in seqtk.
But the extract file contains only the 1st sequence but no others.
I am wondering whether my name.lst file does not fit with what seqtk needs.
I have names of each sequence without other symbols each line in the name.lst. But the fastq file starts each sequence name with a @. Should I add @ in front of each sequence name?
Or what other problem it can be?

Any suggestion is welcome.
Thanks,

Chih-Ming

[vsbuffalo]

Hi Chih-Ming,

I am not the maintainer of seqtk, so take my advice with a grain of salt. subseq does not require '@'s before entries. See this example for usage:

$ echo ">test-1 test\\nGATCTATATGCT\\n>test-2\\nAGTATCATGAGCT\\n>test-3\\nGATTCTTATGCGG" > seqs.fa
$ cat seqs.fa
>test-1 test
GATCTATATGCT
>test-2
AGTATCATGAGCT
>test-3
GATTCTTATGCGG
$ echo "test-1\\ntest-3" > names.lst
$ cat names.lst
test-1
test-3
$ seqtk subseq seqs.fa names.lst
>test-1
GATCTATATGCT
>test-3
GATTCTTATGCGG

Hope this helps.