documentation for making Arrows from Bamfiles for non-10x experiments.

[badoi]

Where is the problematic documentation? The explanation for loading in bamFiles from combinatorial indexing-type snATAC-seq files (e.g. sc-THS-seq from Preissl et al 2018, Lake et al 2017).

1) Improvements can be to have sensible defaults for bamFlag parameter or examples like the gsubExpression. 2) Clarifying that the gsubExpression is to remove non-barcode strings from the bcTag, rather than current documentation. 3) You should create a new section in the user manual in Chapter 1 to walk through loading in bamFiles. Clarification on what kinds of preprocessing is required for the bamFile, e.g. does it need to be pre-filtered, PCR duplicate marked, etc. Sets of parameters for different styles of snATAC-seq out there (sci-ATAC-seq, scTHS-seq, etc).

[rcorces]

Thanks for the suggestion. We will add this in an upcoming release of the website. I will update and close this issue when that is live.

[rcorces]

I'm going to close this now to help tidy up issues. This will go into the next update but is not there yet.