Hi all,
I'm stuck with a total newbie problem here. I'm analyzing RNA-seq data from mouse, I mapped the (paired-end) sequences using TopHat against mm9 (using bowtie1) but when I look at the SAM output files, the hits list chromosomes as map targets, when instead I'm interested in gene IDs. I'm assuming I missed something trivial?
I'm stuck with a total newbie problem here. I'm analyzing RNA-seq data from mouse, I mapped the (paired-end) sequences using TopHat against mm9 (using bowtie1) but when I look at the SAM output files, the hits list chromosomes as map targets, when instead I'm interested in gene IDs. I'm assuming I missed something trivial?
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