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 :
- key 1: Uniquely aligned to isoform1, e.g., in exon1-exon2 junction in SE event
- key 2: Uniquely aligned to isoform2, e.g., in exon1-exon3 junction in SE event
- key 3: Ambiguously aligned to isoform1 and isoform2, e.g., within exon1
- 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]