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hbc / bcbioRNASeq

R package for bcbio RNA-seq analysis.
https://bioinformatics.sph.harvard.edu/bcbioRNASeq
GNU Affero General Public License v3.0
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Support for other count formats #103

Closed ohofmann closed 6 years ago

ohofmann commented 6 years ago

Following up on the Slack discussion: we are mostly relying on STAR and HiSat2 alignments for (low cellularity) tumor RNA-Seq. It would be great if we could use count data generated from these two aligners within the bcbioRNASeq environment, most likely through the express (repo) quantification approach.

mjsteinbaugh commented 6 years ago

Perfect we'll work on adding those to the caller argument of the bcbioRNASeq() constructor.

mjsteinbaugh commented 6 years ago

Hi @ohofmann I'm working on pushing this update. Will ping you when it's done.

mjsteinbaugh commented 6 years ago

Support for caller = "star" or caller = "hisat2" has been added to the pending v0.2.6 release. Internally, this works by loading the featureCounts data from the combined.counts file inside the bcbio project directory.

ohofmann commented 6 years ago

Thanks a lot!