Enabled 10X quantification with STAR-solo (!2) · Merge requests · loosolab / software / scRNAseq.preprocessing

jens.preussner requested to merge starsolo into master Mar 11, 2020

This PR enables quantification of data from 10X using STAR-solo.

Individual features include:

Added STAR mapping for 10X input files (95b765c5, cc678aae)
Refactored code for container creation; now splitted into plate/10X parts (3ba519b4)
Added possibility to have sample metadata in case of 10X (7532002b)
Allowed multiple lanes per sample (2a7f2ddd)
Gathered STAR run statistics in a single table (4eb0d5d2)

and various bug fix commits 😉

Importantly, this PR drops support for kallisto, which was intended previously to quantify UMI data.

Enabled 10X quantification with STAR-solo