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Old 01-15-2014, 05:57 AM   #1
Senior Member
Location: chicago

Join Date: Jul 2012
Posts: 354
Default base position

Is there a script or tool that will identify each base position numbering in a bed file of 1200 amplicons? I am trying to identify homopolymers in an exact position not just a region.
So, if there was a 10-base strech of sequence each nucleotide numbered and identified. A=1,A=2,A=3,A=4,A=5,A=6,T=7,C=8,G=9,C=10. Then a homopolymer of 6A could be found instead of saying there is a homopolmer of 6A in the region 1-10. Thank you.
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Old 01-15-2014, 06:08 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

It's unclear exactly what you want to do, but I imagine that could be done with GenomicRanges in R. Just load the BED file into a GRanges object, use the getSeq() function (or whatever that's called), and then apply() a function to determine if a homopolymer run exists in a given sequence (outputting whatever textual information you want).

The unclear part is what a BED file of amplicons would even mean. BED files just give coordinates of regions in something. If the BED file described bounds for amplicons produced from some larger sequence, then what I wrote above would make sense. Otherwise, describe in more depth what you really mean.
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