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Old 05-15-2012, 05:20 AM   #1
mkbehnke
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Location: Virginia

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Question Getting Illumina export file into R as a GenomicRanges object?

Hello all, I am fairly new to analysis of RNAseq data and have what may be a dumb question, but several hours of searching documentation, google, and this forum haven't helped...

We contracted with a private company to process our samples with Illumina HiSeq, and yesterday I received the output files. However, they sent default output from CASAVA instead of BAM files. I was able to read the export.txt files into R using ShortRead, which creates an AlignedRead object. Now I can't figure out how to turn this into a GenomicRanges object in order to generate counts. it appears that GenomicRanges only works with BAM files, but I've been unable to find a method for either converting the export.txt into .BAM, or converting the AlignedRead object into something GenomicRanges can use.

Help!!

Thanks
Mikki
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Old 05-15-2012, 06:00 PM   #2
Dario1984
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Code:
 readsRanges <- as(alnR, "GRanges")
It takes a long time to get familiar with, but there are lots of useful functions in GenomicRanges.
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Old 05-16-2012, 11:07 AM   #3
mkbehnke
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Thank you so much!
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