Two script files are included.
- barseq.pl : the main script, which is called with various parameters
- barseq.pm : library of functions, loaded into barseq.pl
In general, successive calls to the main script are made, calling the appropriate function and redirecting output to a file, which serves as input for the next step in the pipeline
4 functions can be called, listed in order
- barseq.pl count : input is from a qseq or fastq read file, output is a list of trimmed/truncated reads and their frequency within the file after quality filtering
eg. SH: barseq.pl count het_test_qseq.txt > het_test_readcounts.txt - barseq.pl cluster : input is the readcounts file from 1. Clusters sequences based on mm scoring.
eg. SH: barseq.pl cluster het_test_readcounts.txt > het_test_clusters.txt - barseq.pl map : input is the cluster file from 2, and a list of expected barcodes. This will map the barcodes to the clusters.
eg. SH: barseq.pl map het_test_clusters.txt HET.txt > het_test_map.txt - barseq.pl tabulate : input is the map file from 2, and a list of expected barcodes. This will generate a list of barcodes and the counts for each, with indications on how the mapping was assessed.
eg. SH: barseq.pl tabulate het_test_map.txt HET.txt > het_test_mappedbarcodes.txt