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broadinstitute / CellBender

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
https://cellbender.rtfd.io
BSD 3-Clause "New" or "Revised" License
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New fileformat output from BD rhapsody #359

Open MelanieRN opened 1 month ago

MelanieRN commented 1 month ago

Hi,

BD Rhapsody now outputs the raw counts in the same format as Cell Ranger V3, in a folder with an .mtx file instead of a .csv.gz file. When I use the pipeline on the .mtx file, it recognises it as "Cell Ranger V3 format" instead of BD Rhapsody. Will this affect the results of the analysis, or is it the same pipeline for both BD Rhapsody and Cell Ranger?

carolienv commented 2 weeks ago

Any updates on this issue?