custom technology, barcodes with varying length

[Rémi Montagne]

Hello,

I would like to know if there is a way to analyze custom technology with complex geometry, where the barcodes are in several parts and have varying lengths.

It would be a similar kind of geometry as in some Cel-Seq and InDrop protocols but for a geometry not yet implemented in the list of geometries supported by Kallisto.

Many thanks !

[Pall Melsted]

The -x string can specify where the barcodes, umi and sequences are located. There is a brief description in https://pachterlab.github.io/kallisto/manual (search for "technology in the format") as well as a more complete discussion in https://www.biorxiv.org/content/10.1101/2023.11.21.568164v1.full.pdf (see Box 3).

- Pall

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