extract SNPs corresponding position on BLAST subject sequence
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!
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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 ?