Single vs paired end reads

This tutorial explains how to use YAMP with single- and paired-end reads.

YAMP can handle both single- and paired-end reads just using a single parameter: singleEnd.

The default YAMP behaviour is to use paired-end reads (so singleEnd = false, in ./conf/base.config, please refer to the How to use Nextflow profiles tutorial for details). Therefore if you are using single-end reads you should remember to set it to true.

To set it at run time, you should add either --singleEnd true or --singleEnd false to the command line, as in the two examples below:

• paired-end reads:

nextflow run YAMP.nf --reads1 myfile_R1.fq.gz --reads2 myfile_R2.fq.gz --singleEnd false

• single-end reads:

nextflow run YAMP.nf --reads1 myfile.fq.gz --singleEnd true

Retro compatibility

The way YAMP handles externally single- and paired-end layout has changed in version 0.9.5, and it is no longer compatible with previous versions of the tool. If this is a problem for you, please open an issue and we will try to help.