1.3.0

New Feature

Handle parse split-seq data from experiments with replicates from different split-seq pools that had been built using different illumina multiplexing barcodes from the same initial parse split pool mix. The parse documentation refers to these as sublibraries, and in IGVF we have been calling these subpools.

They different subpools need to be aligned separately cells from different subpools will have colliding cell barcodes. To allow combining different cells from different subpools they have a string representing the different illumina library added.

For libraries processed with this processing pipeline the end result will be barcodes of the form:

<library id>-<2 rounds of cell barcode>_<numeric index>

The parse protocol uses two different barcodes, for one cell. One is used for the polyA primed barcode and one is for the random primed barcode. In most cases it's simplest to combine the two to represent a single count for a gene.

Bug fixes and improvements

• The bulk processing pipeline report had new report options added and some rendering bugs fixed.
• There were various improvements to code to generate sample data for tests.

Full Changelog: 1.2.5...1.3.0

ENCODE 4 scRNA-seq processing pipeline

This contains the final version of the snakemake based pipelines for:

1. scRNA-seq pipeline for 10x RNA and multiome experiments
2. Parse Biosystem's split-seq experimental kit.