I have a FASTA file. I want to extract from some sequence using seqtk. What should be the command for it?

Question

[Mustafa]

I have Fasta fie with 5555 bp. I wanted to extract a small region from 501 to 1532 and run blastn. What should be the code in Seqtk to go about it?

[GenoMax]

Check seqtk subseq. You will need to provide the region you are interested in as BED file. You may also want to use samtools faidx your.fa fasta_header:501-1532.

[Mustafa]

THanks i will try thiss !

Answer 1

[bk11]

You can create a bed file and use it to extract range of sequences you want. Please try something like this.

cat region.bed
chr1    20  50
chr2    10  30

cat input.fasta
>chr1
TGCGGGCGGTGAGGTCGCCCGCCGCGATCGCCTGCAATACCGTCGAGAGCGCGTGCAGATTCGCATCGGAGGTGGCCATC
AATTGATTGAGGCTGTCCACCATCGCGCGGAAGTCGTACTGGAAGCGCTGTGCGTCGCCGCGCACGCTGAAATCGCCATT
GGCTGCGGCCTGCGCAAGCAGCTTGATCTCGCTGTTCATCGCCGACAGGTTG
>chr2
CCCTCCACAGGAAGCGGACCGGACAATGACGCTTGATTGCCGCGCAGGAAATGCCCCCGTTCCCGCAGGCATACACCCCA
TTTGCCGCGGACATACGCCGCACATTTCTCGGAGCCTGGACAAGTCGCCACAGCTTTGATGGAACGACGGAAAAAACGCC
CCGGAGTTGACCAGAACAACCGCCAGTACTGAAATCTGGACCTTAAGTTCCAGTTCCTGCAGCTCTGGACCTGGTTCATC
AGCGAGCTTCTATCGCTTCGCGGCGGCTTCGATCGCAGCGTGTGCGCGCCATCACTTGGTCGTGCGAAATCGTCGGCCGC
GTGTCGGCCACGGCGCGCTCGATCTTCGCCCGGAACTACCAGTCGTAGTCCTCGGCGGCTTCGGTCGACTCAAATTCGGA
AACAGGTGGTCGAGTGATACGCCCAGGGTTC

seqtk subseq input.fasta region.bed >results.fasta

cat results.fasta
>chr1:21-50
GCCGCGATCGCCTGCAATACCGTCGAGAGC
>chr2:11-30
GAAGCGGACCGGACAATGAC

[Mustafa]

Thank you !