Counts reads on genes. Fast. Inspired by htseq-count GenSum support two
quantification methods: union and strict, which are compatible with
htseq-count union and intersection-strict. GenSum and htseq-count produce
identical counts in the union mode, and minor differences in strict mode (1 in
35000 reads). GenSum is much much faster. A 15 million read bam file can be
quantified in around 5s while htseq-count takes about 11 minutes.
For now manually build using the rust toolchain (https://rustup.rs/).
cargo build --release
# binary ends up here:
./target/release/gensum --help
Docker containers for gensum can be found on dockerhub and ghcr.
Required input is a GTF file that contains the exons and the gene-ids. GenSum
uses a very naive parser to extract only 'exon' features. The GTF exon features
are required to have an entry in the attributes that contains: gene_id: "<the gene id to count>". It it recommended to use the files generated by the ensembl
team at: http://ftp.ensembl.org/pub/current_gtf/
The second input is the .bam file created by an aligner. TopHat/HiSat2/STAR
should all work fine. Stranded libraries as well as paired end data are
supported. When using a stranded RNA library supply the library type using the
--strandness flag to restrict counting only the correctly oriented reads.
Paired-end reads are expected to be oriented inwards (--->...<---). Sorting the
bam file by position or name is not required, but paired end reads are stored
until the mate is encountered which can affect memory usage.
USAGE:
gensum [FLAGS] [OPTIONS] --bam <FILE> --gtf <FILE>
FLAGS:
-h, --help Prints help information
-n, --nosingle Do not count paired-end reads that have only 1 mapped end. Default allows one mapped end. Only
affects paired-end reads.
-d, --usedups Also count read (pairs) marked as (optical) duplicate, default excludes duplicates. Requires a bam
files processed with a markdups tool
-V, --version Prints version information
OPTIONS:
-b, --bam <FILE> The bam file to quantify
-f, --gtf <FILE> The .gtf reference transcriptome file
-q, --mapq <0-255> The minimum required mapping quality to include [default: 10]
-o, --output <FILE> The output file
-m, --method <qmethod> The quantification method, 'strict' or 'union'. 'union' counts all genes that
overlap any part of the reads, 'strict' requires the read to map within the exon
boundaries. [default: union] [possible values: union, strict]
-s, --strandness <strandness> The RNA library strandness [F]orward, [R]everse or [U]nstranded [default: U]
[possible values: F, R, U]
The output is a simple two column <tab> delimited file. The first column
contains the gene_id or a descriptive name for unassigned reads. The second
column the counts on that gene.
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