We are currently looking into the viability of Digital Gene Expression (DGE) or mRNA-seq as a possible replacement for expression microarrays in our breast cancer studies. DGE generates reads that are only 17 bases in length, and thus allowing for even 1 mismatch is a little questionable when aligning against the human genome. MAQ doesn't seem to allow you to specify the -n flag as anything less than 1 - is this something that can be altered easily? I would love to align my short reads via MAQ but only keep those that align perfectly.
Along those lines, if a read maps to more than 1 location, MAQ will randomly pick one of those locations for the placement of that read. Is there any way to customize this function so that it checks against a coordinate file or something like that so we can at least have MAQ select a location for that read that is only in the transcriptome to raise our chances of the placement being 'correct'?
Thank you for your help
Along those lines, if a read maps to more than 1 location, MAQ will randomly pick one of those locations for the placement of that read. Is there any way to customize this function so that it checks against a coordinate file or something like that so we can at least have MAQ select a location for that read that is only in the transcriptome to raise our chances of the placement being 'correct'?
Thank you for your help
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