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