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Since Karma uses the word size and occurrence cutoff to help construct the actual index and hash filenames, you must specify them the same way you did when you created the reference index and hash.
Since Karma uses the word size and occurrence cutoff to help construct the actual index and hash filenames, you must specify them the same way you did when you created the reference index and hash.
== Options for aligning reads ==
-a [int] -> maximum insert size
-B [int] -> max number of bases in millions
-E -> show reference bases (default off)
-H -> set SAM header line values (e.g. -H RG:SM:NA12345)
-o -> required output sam/bam file
-O [int] -> occurrence cutoff (default 5000)
-q -> quiet mode (no output except errors)
-r [name] -> required genome reference
-R [int] -> max number of reads
-w [int] -> index word size (default 15)
== Aligning Reads (Illumina) ==
== Aligning Reads (Illumina) ==
