Getting Illumina export file into R as a GenomicRanges object?

[mkbehnke]

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

[Dario1984]

 readsRanges <- as(alnR, "GRanges")

It takes a long time to get familiar with, but there are lots of useful functions in GenomicRanges.

[mkbehnke]

Thank you so much!