Allele specific expression in RNAseq - masked genome

[rodrigo.duarte88]

Dear folks,

My lab is specialised in allele specific expression. We made allele specific expression measurement in a targetted polymorphism and found allele A 12% more expressed than allele T. When we RNAseq'd this sample, I mapped the reads only to the chromosome where the SNP is found, and found allele specific expression measurement inverted (allele T 12% more expressed than allele A).

I am aware of the famous RNAseq bias. So because of computational limitation, I tried mapping my reads against a "masked" chromosome 10 (that I found on http://hgdownload.cse.ucsc.edu/golde...38/snp142Mask/ ).

This analysis ran for over 2 weeks on my poor octa-core computer. I tried uploading all these files to Galaxy too, and the server knocked down this task saying it exceeded the time limit.

So:
1- Is all this totally wrong and I should follow a completely different approach?
or
2- Is it time to cry for a cluster and try over there the read mapping against the masked genome/chromosome?


Thanks a lot for your kindness in following this until the end.