Repo for bliss pipeline
bash ./bin/bliss.sh expName human ./patterns/patfile-name MapQuality /home/garner1/Work/dataset
Where the parameters could be like these:
expName = "MN30" (specify the name of the experiment)
human = "human" (specify the genome)
./patterns/patfile-name = "./patterns/BB101_Milan-5-04_CATCAATC" (location of the file containing UMI and barcode specs)
MapQuality = "30" (mapping quality threshold)
/home/garner1/Work/dataset = (location of the dir containing the fastq files)
NOTE that some parameters, like the number of processors, are hard-coded in the ./bin/bliss.sh script.
Requires (at least):
gnu parallel
scan_for_matches