Visium reader requires file names not present in spaceranger output
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ilia-kats commented
The count matrices, as written by SpaceRanger, are always called filtered_feature_bc_matrix.h5
, both in SpaceRanger 1 and SpaceRanger 2. This is also stated in the 10x docs. However, the current Visium reader looks for something_filtered_feature_bc_matrix.h5
and fails.
As a sidenote, it would be good to optionally also be able to read in the raw_feature_bc_matrix.h5
. Sometimes, when doing QC, it helps plotting them side-by-side to judge the levels of ambient RNA in the sample.