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:

• Trim the sequence ID before a space (e.g., “comp18530_c0_seq1 len=1406 path=[683:0-1405]” would instead be represented as “comp18530_c0_seq1”).
• Define the minimum match length to include the read (e.g., all matching reads smaller than some specified value, such as 25 base pairs, can be excluded from the output table).
• Count paired end reads as only a single match. (Although there might be two paired reads, these represent only one single underlying nucleotide fragment).

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