Feature request: CRAM input support

[matthdsm]

Hi,

To be able to use saseR in our nf-cmgg pipelines we could like to be able to use cram files as input.
Is this something that seems feasable to you?

Thanks
Matthias

[mvheetve]

Hej there!

You can find out how to generate count matrices with bam files as input here: https://bioconductor.org/packages/devel/bioc/vignettes/saseR/inst/doc/saseR-vignette.html#transforming-bam-to-count-matrices.

Alternatively, you can use any count matrix (from Salmon, Kallisto or Rsubread for example) as input.

Or are you asking for a cram support implementation?

Welcome
Mattias

[matthdsm]

I'm asking for cram support as the Rscript included with the vignette and the docs only speak of bam files.

Thanks

[mvheetve]

We"ll look into it, thank you for the suggestion.