How to use with many bam files?

In the documentation, there is a command to perform velocyto run on a single bam file, but how would you do this for 100s of cells at a time? Do you recommend aggregating all the bam files together and adding a unique ID to the “read_group” field?

[gioelelm]

You can do that in a second step using loompy.combine Notice that the function will combine the files without the need of loading the full matrixes into memory.

If you want to do this from the command line you can simply put together a simple script, something like the following should do:

import sys
import loompy

loompy.combine(sys.argv[1:-1], sys.argv[-1])
# usage: script.py file1.loom file2.loom file3.loom merged.loom

[ChelseaCHENX]

Great, thanks for the info and script. By any chance, do you know if the cell barcodes will be modified to reflect the sample of origin? Thanks again for your help. Fernando

It has been an old issue - but would like to comment on this - I suppose in the current version of run10X the barcodes are modified (adding the name of the sample) CertainSample:AAACCCAAGCTATCCAx? Would this affect the merging step? Thx!