Counts read hits against a reference gene set

View the Project on GitHub mpcox/mapcount


The Perl program mapcount counts next generation sequencing reads that map against a reference gene set.

mapcount extracts a list of expected sequence IDs from a user-provided FASTA file (such as a file of gene models). It then parses a user-provided mapping file in the standard SAM format and counts the number of reads that map to each gene. Tabular output is written to a user-defined text file.

Optional flags allow the user to:

Program usage is as follows:

map_count -f|fasta FASTA file -s|sam SAM file -o|output text file 
         [-t|trim] [-l|length 25] [-p|pair]
Required flags:
-f|fasta    FASTA reference file
-s|sam      SAM mapping file
-o|output   tabular text file
Optional flags:
-t|trim     trim ID to entry before first space
-l|length   minimum match length for inclusion in the count table
-p|pair     count paired matches as one match