You can either iterate over the
prefix.bam file N times or use
--split-bam. Each barcode has its own BAM file called
The optional parameter
--split-bam-named, names the files by their barcode names instead of their barcode indices. Non-word characters, anything except [A-Za-z0-9_], in barcode names are replaced with an underscore in the file name.
This mode might consume more memory. Read the next FAQ entry for more information.
In addition, a
prefix.datastore.json is generated to wrap the individual dataset files.
Input barcode sequences are tagged with an incrementing counter. The first sequence is barcode
0 and the last barcode
numBarcodes - 1.
If you use output BAM splitting, it can happen that you get a lot of output files. Using
--files-per-directory N creates subdirectories and outputs at most
N barcodes per directory.