extract SNPs corresponding position on BLAST subject sequence
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5.0 years ago
pbigbig ▴ 240

Hi everyone,

I have run BLAST a transcript containing SNP against genome and get result like this (outfmt6)

TRINITY_DN25200_c0_g1_i2@4719A--T   scaffold75_cov195   99.031  3303    15  4   1506    4807    13900341    13903627    0   5906

Since the position of SNP is 4719 on the transcript, could you tell me how to transfer the notation [A/T] to corresponding position on the genome and then extract genomic sequence with flankings of 400bp around this SNP? I would prefer the automatical way applied for multiple instances but I was limited in programming skill.

Thank you very much in advance for your help!

SNP BLAST extract sequence • 1.7k views
Entering edit mode

It's not clear in your question what the transcript is, what the genome reference build is, or what the various fields are in your printed line...?

Have you taken a look at this thread: Get Flanking Sequence Given A List Of Positions ?


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