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alexdobin / STAR

RNA-seq aligner
MIT License
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Solo.out/Gene/raw/UniqueAndMult-{EM,PropUnique}.mtx includes zero-count entries #1628

Open ScottNortonPhD opened 2 years ago

ScottNortonPhD commented 2 years ago

When running STARsolo with --soloMultiMappers Uniform PropUnique EM Rescue, four additional .mtx files are generated in the same directory as the default matrix.mtx. These four matrices all contain the same matrix coordinates as each other, but for the EM and PropUnique, some of those values are zeros. This is not a serious bug as the output is still usable, however it does take up unnecessary disk space to report explicit zeros in what should be a sparse matrix format.

alexdobin commented 2 years ago

It makes it easier to compare different multi-gene schemes. The zero-count lines can be filtered out in the post-processing if needed.