brie-count CLI

BRIE (>=2.0.0) provids two CLI directly available in your Python path: brie-count, brie-quant.

Splicing annotations

As input, it requires a list of annotated splicing events. We have generated annotations for human and mouse. If you are using it, please align RNA-seq reads to the according version (or close version) of reference genome. Alternatively, you can use briekit package to generate.

Read counting

The brie-count CLI calculates a count tensor for the number of reads that are aligned to each splicing event and each cell, and stratifies four them into four different categories in :

  1. key 1: Uniquely aligned to isoform1, e.g., in exon1-exon2 junction in SE event
  2. key 2: Uniquely aligned to isoform2, e.g., in exon1-exon3 junction in SE event
  3. key 3: Ambiguously aligned to isoform1 and isoform2, e.g., within exon1
  4. key 0: Partially aligned in the region but not compatible with any of the two isoforms. We suggest ignoring these reads.

Then you fetch the counts on a list of bam files by the command line like this:

brie-count -a AS_events/SE.gold.gtf -S sam_and_cellID.tsv -o out_dir -p 15

By default, you will have four output files in the out_dir: brie_count.h5ad, read_count.mtx.gz, cell_note.tsv.gz, and gene_note.tsv.gz. The brie_count.h5ad contains all information for downstream analysis, e.g., for brie-quant.

Options

There are more parameters for setting (brie-count -h always give the version you are using):

Usage: brie-count [options]

Options:
  -h, --help            show this help message and exit
  -a GFF_FILE, --gffFile=GFF_FILE
                        GTF/GFF3 file for gene and transcript annotation
  -S SAMLIST_FILE, --samList=SAMLIST_FILE
                        A tsv file containing sorted and indexed bam/sam/cram
                        files. No header line; file path and cell id (optional)
  -o OUT_DIR, --out_dir=OUT_DIR
                        Full path of output directory [default: $samList/brieCOUNT]

  Optional arguments:
    -p NPROC, --nproc=NPROC
                        Number of subprocesses [default: 4]