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If I have sequence start and end coordinates, how can I get the sequence from local hg19.fa file. Either using samtools or perl will be good for me.
hg19 has been indexed using samtools.
Thanks!
hg19 has been indexed using samtools.
Thanks!
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You can use the same command you used to index the fasta. That is, construct the index:Originally posted by lewewoo View Post
Then extract your subsequence:Code:samtools faidx hg19.fa
You'll have to adjust the coordinates and chromosome for what you want. There is also a Perl package for working with SAM/BAM files that may be helpful if you have a lot of operations to perform.Code:samtools faidx hg19.fa 1:20-200
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thanks
will try it
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Or you can use seqret in Emboss. You do not need to index your reference.Comment
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