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I have about 300 90-bp sequences which I would like to map to a reference genome to make it longer to a 300bp sequence, wherein the 90bp is at the middle.

Anyone knows what bioinformatics tool I can use for this? Thank you!

Actual scenario: The SNP sequences are from a SNP panel data (90bp sequence, SNP is at the middle). We would like to extend the sequence to 300bp, retaining the SNP at the middle so we can make a sequence capture panel of the SNP.

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  • $\begingroup$ You mean the target capture panel of SNP markers? $\endgroup$
    – envs_h_gang_5
    Jun 29, 2022 at 6:38
  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Jun 29, 2022 at 12:41
  • $\begingroup$ @envs_h_gang_5 I'm actually not very familiar, but something like 'genotyping by sequencing' kind of panel. $\endgroup$
    – Umi Rayearth
    Jul 1, 2022 at 4:17

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If you have a SNP panel then you have the coordinates on the genome. You can use tools such as bedtools slop to expand the coordinates to the desired length and then extract those regions from the target genome using bedtools getfasta.

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  • $\begingroup$ Thank you! That's very helpful. The dilemma, however, is we'd like to extract the 300bp sequences from a different genome, and not from the reference genome of the SNP panel, therefore the coordinates on the SNP panel will not be exactly on our genome. $\endgroup$
    – Umi Rayearth
    Jul 1, 2022 at 4:20
  • $\begingroup$ Then you need liftover genome.ucsc.edu/cgi-bin/hgLiftOver I don't know if the genomes you're working on have mapping files though. $\endgroup$
    – asafpr
    Jul 1, 2022 at 7:51

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