rmapbs-pe input

[bio15anu]

Hi,

I have compiled rmap from bioconda on macOS X and am trying to run rmapbs-pe specifically on simulated data. The guide mentions that paired-end data should be concatenated into a single input file but the program will not accept this when it is run for example like this:

rmapbs-pe -c genome.fa -o output.bed input.fastq

This simply outputs the -help information.

When the paired-end files are instead given separately the program will run, but even with only 10 reads it never reaches completion.

rmapbs-pe -c genome.fa -o output.bed pe_1.fastq pe_2.fastq

Can anybody provide any ideas for how I could get this to run properly?