extract SNPs corresponding position on BLAST subject sequence
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4.2 years ago
pbigbig ▴ 230

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 • 1.6k views
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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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