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-   -   Allele specific expression in RNAseq - masked genome (http://seqanswers.com/forums/showthread.php?t=58490)

rodrigo.duarte88 05-12-2015 04:04 AM

Allele specific expression in RNAseq - masked genome
 
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. :D


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