Dealing with Paired End Files

[SayanNanda]

Is there any method in place to do the FMAP_mapping.pl step for paired end fastq files? Is giving both the files as parameters for the perl script sufficient or is there any other way to go about this?

[jiwoongbio]

"FMAP_mapping.pl" does not provide the function considering paired-end read information. If you have done de novo metagenome assembly, I recommend to use "FMAP_assembly.pl" instead.