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
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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