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broadinstitute / epi-SHARE-seq-pipeline

Epigenomics Program pipeline to analyze SHARE-seq data.
MIT License
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Changes to how to call starsolo #36

Closed nchernia closed 2 years ago

nchernia commented 2 years ago
emattei commented 2 years ago

I am guessing you removed the filtered outputs because you want to filter those yourself but could you leave the h5 matrix raw? It is created very efficiently so it saves us an extra script.

Another thing to consider is that if we don't get the filtered alignments we lose the genes quantification right? I would love to get everything we need out of starsolo if possible. If not, so be it.

nchernia commented 2 years ago

There is no h5 matrix created by star solo.

No, filtered vs raw is just like cell ranger’s definition of filtered. We can load barcodes, genes, matrix into Seurat with one command and do our own filtering (best to use the atac to filter the rna and maybe some filters on nUMI and nGene)

On Fri, Aug 12, 2022 at 10:15 PM Eugenio Mattei @.***> wrote:

I am guessing you removed the filtered outputs because you want to filter those yourself but could you leave the h5 matrix raw? It is created very efficiently so it saves us an extra script.

Another thing to consider is that if we don't get the filtered alignments we lose the genes quantification right? I would love to get everything we need out of starsolo if possible. If not, so be it.

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