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mhammell-laboratory / TEtranscripts

A package for including transposable elements in differential enrichment analysis of sequencing datasets.
http://hammelllab.labsites.cshl.edu/software/#TEtranscripts
GNU General Public License v3.0
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outSAMmultNmax #125

Closed imerelli closed 2 years ago

imerelli commented 2 years ago

Hi, I'm wondering if setting the --outSAMmultNmax parameter of STAR can impact the analysis (while the parameters --winAnchorMultimapNmax and --outFilterMultimapNmax are discussed, there is no information about --outSAMmultNmax).

olivertam commented 2 years ago

Hi,

--outSAMmultNmax dictates how many alignments are outputted to SAM/BAM after running STAR. By default, it is set to -1, which means output all alignments found. Setting this to another value would simply restrict the number of alignments that are reported (the total number of alignments found will still be indicated in the NH:i: tag), and thus could remove alignments that were found and required for accurate quantification.

Thus we recommend leaving it at the default value.

Thanks

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