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Mar 13, 2023
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update readme #207

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3 changes: 1 addition & 2 deletions README.md
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Expand Up @@ -4,8 +4,6 @@
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Expand All @@ -28,6 +26,7 @@ This is a community effort in building a pipeline capable to support:
- STARSolo
- Kallisto + BUStools
- Cellranger
- UniverSC

## Documentation

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6 changes: 4 additions & 2 deletions docs/usage.md
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Expand Up @@ -50,12 +50,14 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p

### Expected cells

This parameter may be used for three of the four supported aligning options.
This parameter is currently supported by

- [Salmon Alevin](https://salmon.readthedocs.io/en/latest/alevin.html#expectcells)
- [Cellranger](https://software.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/release-notes) - NB: Current recommendation is to use auto-estimation of expected cells
- [STARsolo](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md)

In the future, support for this paramter will be added to cellranger and UniverSC. Note that since cellranger v7,
it is not recommended anymore to supply the `--expected-cells` parameter.

## Aligning options

By default, the pipeline uses [Salmon Alevin](https://salmon.readthedocs.io/en/latest/alevin.html) (i.e. --aligner alevin) to perform pseudo-alignment of reads to the reference genome and to perform the downstream BAM-level quantification. Then QC reports are generated with AlevinQC.
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