I have a FASTA file. I want to extract from some sequence using seqtk. What should be the command for it?
1 answer
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
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Check
seqtk subseq. You will need to provide the region you are interested in as BED file. You may also want to usesamtools faidx your.fa fasta_header:501-1532.THanks i will try thiss !