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Include --expect-cells when using --aligner cellranger #182

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adairama opened this issue Nov 11, 2022 · 2 comments
Open

Include --expect-cells when using --aligner cellranger #182

adairama opened this issue Nov 11, 2022 · 2 comments
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enhancement New feature or request

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@adairama
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Description of feature

As discussed in the Slack Channel for scrna-seq on 23rd September 2022:

It will be good to allow --expect-cells in the run with --aligner cellranger option for scrnaseq pipeline. Since the expected cells can vary between samples (e.g. 6000 for sample 1, 3000 for sample 2), it will be good have this as a column in the sample metadata.

Gregor Sturm suggested related issue:
#90 (comment)

@adairama adairama added the enhancement New feature or request label Nov 11, 2022
@apeltzer
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CellRanger v.7 (which is included inthe pipeline) should auto-detect this btw, so actually not really needed. Not sure if its more accurate if we specify it (and what happens if we specify a wrong value here?).

@grst
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grst commented Mar 13, 2023

also universc should consume the expected_cells column. I suggest to add a value auto as default for cellranger.

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