Options for clc_unmapped_reads
usage: clc_unmapped_reads <options>
Extract unmapped reads from a read mapping.
Options:
-h / --help: Display this message.
-a <file> / --cas <file>: Specify the input cas file (required).
-o <file> / --output <file>: Specify the output fasta or fastq file
(required).
-l <n> / --minlength <n>: Output only sequences with a certain minimum
length.
-u / --unaligned: For matching reads with sufficiently long unaligned parts,
output these parts as individual sequences. Two parts may be output if
both ends are long enough. Must be used with the '-l' option.
-p / --paired: Always treat the reads as paired, so if one read of a pair
qualifies for reporting, report both reads. Cannot be used with the "-u"
option.
Example:
Make a fasta file with all the unmapped reads along with all read parts
that were unaligned and has a length of at least 100 bp:
clc_unmapped_reads -a mapping.cas -o unmapped.fasta -l 100 -u