Mapping sgRNA counts for cas12 6-plex CRISPR screens
How to install cargo
```bash
cargo install casmap
git clone https://github.com/noamteyssier/casmap cd casmap cargo install --path . ```
This requires 2 fastqs - an R1 and a R2. These can be gzipped or plaintext.
This will also require a spacer table which is a 3 column tab-delim table.
The columns represent [sequence, construct_id, ordering]. The construct
id and the ordering currently must be numeric.
text
ATGACGAGCTGAGAGCAAGAGCG 0 0
GAAGTCGGGTGGGCGGGGTCATT 0 1
CGCCGCTTCTACATAGTATCGTT 0 2
GAGTTCTGTCCCTCTGCACTTGC 0 3
TTATGAATCTAATGCCCGTCGGA 0 4
TTTAGCTTCGCCTTCGGGATTCA 0 5
GGAGCGAAGTAAACCCGTTGCGA 1 0
TGCAATCACCGCGCTGAGAAATG 1 1
AATGAGCATAAAAGCGATTTAAA 1 2
CATCTGCTCGACTAGTCGGTAAA 1 3
ATCCACGCTGTATACTAAAATTG 1 4
CGCGCACATCATGGTGCTTATCC 1 5
This will also require a constants table representing the static regions
between the variable spacers.
It is a two column tab-delim table representing [sequence, ordering].
Currently the ordering must be numeric.
text
TACCGTTCACATCGATTTT 0
CGGCCCCATGTGCAAGTAT 1
AAAGAGGCAATTGGTCAAA 2
ATTACAGCCGCAACAGGTC 3
GTGCCCGGTTTAGGTTAAT 4
TGCGAATTTTTGGCTGATC 5
To have some dummy data to test the interface you can use my sequence simulator: casgen
```bash
cargo install casgen
casgen ```
This will map constructs with exact matching on both the spacers and constant regions.
bash
casmap constructs \
-i casgen_R1.fastq \
-I casgen_R2.fastq \
-s casgen_spacers.tsv \
-c casgen_constants.tsv
This will write which spacers each read maps against and the number of of each spacer mapped.
bash
casmap spacers \
-i casgen_R1.fastq \
-I casgen_R2.fastq \
-s casgen_spacers.tsv
This will map constructs by matching spacer tuples and ignoring constant regions. It will also allow unambiguous one-off mismatches when mapping spacers.
bash
casmap tuples \
-i casgen_R1.fastq \
-I casgen_R2.fastq \
-s casgen_spacers.tsv