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sjroth / ARTDeco

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How does ARTDeco Handles multi-mapped reads? #18

Closed paulocaldas closed 1 year ago

paulocaldas commented 1 year ago

Hi,

I have just a quick question. I was trying to figure out how ARTDeco deals with multimapped reads in the bam files?

The reason this is relevant for me is because I tried to run ARTDeco on 100+ bam files aligned with STAR using the option --outFilterMultimapNmax set to 10 (default) and then set to 1 (only allowing for unique aligned reads) and I got roughly the same number of expressed genes and number of DoGs. I'm tryin to figure out the reason the results don't change at all (which is actually not a bad thing if it the case)

Cheers, Paulo

sjroth commented 1 year ago

Hi Paulo,

Multimappers are handled by HOMER. When creating a tag directory (the basic data structure of reads), by default, multimappers are tossed out (only uniquely mapped reads are used; description here: http://homer.ucsd.edu/homer/ngs/tagDir.html). This is part of the difference in performance between DoGFinder and ARTDeco.

Hope this helps, Sam

paulocaldas commented 1 year ago

Great! Thanks for the quickly reply ;)