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smithlabcode / ribotricer

A tool for accurately detecting actively translating ORFs from Ribo-seq data
http://doi.org/djv4
GNU General Public License v3.0
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Question about Multi-Mappers #160

Closed singhbhavya closed 2 months ago

singhbhavya commented 2 months ago

Hi there,

I've come to understand that the program does not handle multi-mappers. For our purpose of looking at TE elements (which often have multimapping due to very similar reads), we need to allow for this. If the BAM files were generated with multi-mappers, can they still be run through the program? Does RiboTricer pick the alignment with the highest quality & mapping score?

saketkc commented 2 months ago

Yes, they can still be run through the program. The recommendation for only keeping unique reads is for computational efficiency (larger bam -> more time to parse). We only use uniquely mapping reads (tracking the sam flags) for all downstream processing. Hope this helps!