dgcount

Dual guide CRISPR counting

Installation

cargo install dgcount
dgcount --help

Usage

This expects as input a library file and at least one sample file (in binseq format).

The library is a 4 column TSV without a header with columns:

1. guide pair name
2. gene pair name
3. protospacer 1
4. protospacer 2 (reverse complement)

This assumes that all protospacer sizes are equal.

The sample is expected to be paired and this assumes that the secondary sequence is reverse complemented from the sequencer.

The protospacer can be placed anywhere within the read in both the R1 and R2 and this is robust to stagger sequencing.

The algorithm first indexes the input library and finds expected protospacer pairs. It then scans each record for protospacer sequences, if there is one in both primary and secondary sequence and that combination is expected, then the guide pair count is incremented.

Multiple samples can be provided at the CLI and a counts table is generated including all samples.

dgcount library.tsv sample1.bq sample2.bq sample3.bq

Note: By default dgcount will match unambiguous one-off mismatches to the library. If you want only perfect matches then use the -xor --exact flag.