Paired readsPaired reads often come split across two files: one containing the first mates,
and one containing the second mates,
-p/--paired parameter to indicate that the following files contain paired reads of a certain type, and use the
-i/--interleave parameter to pair up the two files:
clc_mapper -q -p fb ss 50 500 -i paired_1.fa paired_2.fa ...Behind the scenes, the pairs are interleaved and processed together:
If you have a paired file, that is already interleaved, you can leave out the
clc_mapper -q -p fb ss 50 500 interleaved_pairs.fastq ...For detailed information about the
-p fb ss 50 500parameter, please refer to Paired read considerations.