-M parameter has to be set to 1.12 to predict transcript?

[JanaSperschneider]

Hi there,

this is related to issue #324

I have a bam file of a region that covers a known gene, but stringtie 3.0.1 does not return a transcript unless I set -M 1.12 or greater.

My understanding is that -M should range from [0-1] where 0 means only uniquely mapped reads in bundle and 1 means bundle consisting only of multi-mapped reads? Would be great if this could be clarified in the documentation.

The only other way to get a transcript called with my bam file is by changing all the 'NH:i:2' tags to 'NH:i:1', so this issues indeed seems related to the fraction of multi-mapped reads.

Thanks for your help!
Jana