Entering edit mode
Hi,
I am examining a sample on a MCF-7 cell line (of paired-end RNA seq data including the SNP array data) where I want to investigate the allelic imbalance Genome Wide, not just one specified region (for example: "searchArea"). This way, I could find genes where allelic imbalance occur instead of the other way around. I was wondering if the AllelicImbalance package allows more than one seqlevel for each BAM file. And what will be the alternative solution to this problem?
Kind regards,
Sandra