eland codes for unmapped reads?

jayoung · 04-27-2011, 05:57 PM

Hi,

I'm analyzing some Illumina data (HiSeq) using Bioconductor and am curious to look a little bit more at the unmapped reads.

We're interested in some segmentally duplicated regions, so I'm curious to see whether I can use Illumina's mapping codes to see which of the unmapped reads didn't match anything at all, and which mapped to multiple locations.

Can anyone point me towards documentation on what the ELAND mapping codes mean for reads that didn't map to a chromosome? (e.g. NM, 255:255:255, 1:71:255, 0:1:0 etc). I suspect there's some useful information there but I don't know what it means.

I'm fairly new to next-gen sequence analysis - apologies if there's an obvious place to find this that I'm ignoring.

thanks very much,

Janet Young

Fred Hutchinson Cancer Research Center,
Seattle, WA, USA

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04-27-2011, 05:57 PM	#1
jayoung Junior Member Location: Seattle, WA, USA Join Date: Apr 2011 Posts: 1	eland codes for unmapped reads? Hi, I'm analyzing some Illumina data (HiSeq) using Bioconductor and am curious to look a little bit more at the unmapped reads. We're interested in some segmentally duplicated regions, so I'm curious to see whether I can use Illumina's mapping codes to see which of the unmapped reads didn't match anything at all, and which mapped to multiple locations. Can anyone point me towards documentation on what the ELAND mapping codes mean for reads that didn't map to a chromosome? (e.g. NM, 255:255:255, 1:71:255, 0:1:0 etc). I suspect there's some useful information there but I don't know what it means. I'm fairly new to next-gen sequence analysis - apologies if there's an obvious place to find this that I'm ignoring. thanks very much, Janet Young Fred Hutchinson Cancer Research Center, Seattle, WA, USA