Closed KhudyakovLab closed 8 years ago
You need to create a file of the sequence IDs you want to keep, say ids.txt
, then run seqtk subseq file.fa ids.txt
.
To get the ids.txt
you can use standard unix tools like grep
and sed
and cut
.
eg. grep c1_g1_i file.fa | sed 's/^.//' > ids.txt
Hi,
I am trying to use seqtk to extract fasta sequences of specific genes from a transcriptome assembly. I have a list of gene names (example: TR1234|c1_g1). In the assembly file, some of the genes contain several isoforms (TR1234|c1_g1_i1 and TR1234|c1_g1_i2). I would like to extract ALL the isoforms for each of the genes in my list. I tried using a list with wildcards for isoforms (i.e. TR1234|c1_g1_i*) but this did not work. Does anyone have any suggestions for how to deal with this issue?
Thanks so much, Jane