Can I split my data by barcode?

You can either iterate over the prefix.bam file N times or use --split-bam. Each barcode has its own BAM file called prefix.idxBest--idxCombined.bam, e.g., prefix.0--0.bam.

The optional parameter --split-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.

How do barcode indices correspond to the input sequences?

Input barcode sequences are tagged with an incrementing counter. The first sequence is barcode 0 and the last barcode numBarcodes - 1.

Can I limit the output files per directory?

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.

Split barcodes into own sub-directories

Since v2.5.0 each barcode can be stored in its own sub-directory: --split-subdirs. A parent XML will point to all of the barcoded files.

Output missing barcodes

If you have provided bio samples with barcode pairs, option --output-missing-pairs allows to create empty barcode files in all split modes.