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alexyermanos / Platypus

R package for the analysis of single-cell immune repertoires
GNU General Public License v3.0
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Does not detect `sample_filtered_feature_bc_matrix` GEX output from `multi` #19

Closed aseyedia closed 2 years ago

aseyedia commented 2 years ago

https://github.com/alexyermanos/Platypus/blob/75aceffd2cf54a48bd2513fdc083c01894cdea46/R/VDJ_GEX_matrix.R#L1296-L1312

Hi,

I am trying to load VDJ-B, VDJ-T and GEX outputs from Cell Ranger multi with VDJ_GEX_matrix() and it appears that perhaps Cell Ranger 7 has updated the output directory names, because VDJ_GEX_matrix() aimed at multi output's outs directory produces the following error:

The GEX directory filtered_feature_bc_matrix or sample_feature_bc_matrix was not found at the given path. Please revise GEX input pathsDone with GEX pipeline

However, the relevant directory is named sample_filtered_feature_bc_matrix.

Setting the h5 to sample_filtered_feature_bc_matrix using GEX.read.h5 works.

vickreiner commented 2 years ago

Hi! Thanks for letting us know! We always try to keep up with the Cellranger's innovations in folder naming. I will add the sample_filtered_feature_bc_matrix to the path-completion options.

vickreiner commented 2 years ago

Update pushed to the Platypus/R folder. Will be integrated in the next build Thanks again!