Hello everybody. I just wanted to ask if somebody has any experience in aligning sex specific data to hg19 genome build. I recently came accross a weird problem (which when you look at it indepth makes more sense) wherein I aligned my transcriptome sequencing data from primary breast cancer tumours to hg19, and a lot of the reads (approx 15000) were actually aligning to the y chromosome. I am using tophat 2.0 and bowtie 2.0 for the alignment.
Has anybody faced this issue previously? Does it make sense to create a custom sex specific reference by removing the Y chromosome if your sequencing sample is female? I know 15000 is too small a percentage of reads when compared with the entire transcriptome having millions of reads, all the same this is an interesting question. Or is it that it really dosent matter a lot, and I am making a mountain out of a molehole? ANy thoughts would be mightily appreciated! thanks
Has anybody faced this issue previously? Does it make sense to create a custom sex specific reference by removing the Y chromosome if your sequencing sample is female? I know 15000 is too small a percentage of reads when compared with the entire transcriptome having millions of reads, all the same this is an interesting question. Or is it that it really dosent matter a lot, and I am making a mountain out of a molehole? ANy thoughts would be mightily appreciated! thanks

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