meRanTK User Manual
meRanTK change log (text file)
meRanTK is written in Perl and requires Perl 5.10 or newer installed on your computer. Standalone executables for Linux x86_64 are provided. They should run out of the box, without any further requirements.
Since meRanGs is using 2 instances of the STAR aligner, running out of memory can occur, especially when working with large genomes (e.g. human or mouse). To keep the index for these genomes in memory STAR requires ~2x30GB of RAM.
In case you have enough RAM, you could check if your system account has a memory limit set (use the ulimit command). If so, then you should try to remove the limit or ask your system administrator to do so.
In case you don't have enough RAM on your compter, please try to use meRanGh instead. meRanGh is using HiSat2 which requires significantly less memory.
You can run meRanGs and meRanGh on multiple CPUs by specifying "-t x", where x is the number of CPUs you want to use.
You can run meRanCall on multiple CPUs by specifying "-p x", where x is the number of CPUs you want to use. meRanCall dramatically benefits from parallel processing. The more the better :-)
You may use meRanT, which can use a reference "transcriptome" to map the reads. E.g. refSeqRNA or tRNAs
You will need to install the libgd2 package on your system
YES, meRanGs was always able to align such reads (-dt option). The same is true for meRanGh which replaces meRanGt (meRanGt is deprecated since version 1.2.0). Dovetailing read pairs however might indicate a suboptimal sequencing library and they should be carefully inspected.
dietmar . rieder [ at ] i-med . ac . at