casmap
Mapping sgRNA counts for cas12 6-plex CRISPR screens
Installation
How to install cargo
# from crates.io
# from github
Inputs
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.
Spacer Table
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
Constant Table
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.
TACCGTTCACATCGATTTT 0
CGGCCCCATGTGCAAGTAT 1
AAAGAGGCAATTGGTCAAA 2
ATTACAGCCGCAACAGGTC 3
GTGCCCGGTTTAGGTTAAT 4
TGCGAATTTTTGGCTGATC 5
Dummy Data
To have some dummy data to test the interface you can use my sequence simulator: casgen
# install
# run
Usage
Construct Counting
This will map constructs with exact matching on both the spacers and constant regions.
Spacer Characterization
This will write which spacers each read maps against and the number of of each spacer mapped.
Tuple Counting
This will map constructs by matching spacer tuples and ignoring constant regions. It will also allow unambiguous one-off mismatches when mapping spacers.
Describe
This will map the spacers and direct repeats foun for each one of the reads and report back a tab-separated value table for each read.