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