search

GoekeLab / bambu

Reference-guided transcript discovery and quantification for long read RNA-Seq data
GNU General Public License v3.0
190 stars 24 forks source link

recommended quality control for input BAM files #418

Open sparthib opened 8 months ago

sparthib commented 8 months ago

Hi, I am just wondering if there is a recommended QC steps that is recommended for input bams? For e.g. recommended MAPQ threshold for minimap, removing supplementary reads, etc. ?

Thanks,

Sowmya

andredsim commented 8 months ago

Hi Sowmya,

In our pipelines we do not do any extra filtering or QC and use the minimap2 output directly. We do purposely keep supplementary reads in, in the event of fusion genes, however you can remove these if this is not a concern for you. I hope this helps.

Kind Regards, Andre Sim