How to run YAMP with QC'ed reads

This tutorial explains how to run YAMP using reads that have externally QC'ed.

If you have a single file

If you are working with a single-end layout, or your forward and reverse QC'd reads are stored in a single file (as done by YAMP), you should call YAMP with the following instruction:

nextflow run YAMP.nf --reads1 QC_reads --singleEnd true --mode characterisation

where QC_reads represents the path to the raw data and singleEnd is used to tell YAMP that you are providing a single file in input.

Please note that the command line may include further options, such as --prefix or --outdir.

If you have two files

If you are working with a paired-end layout and your QC'd forward and reverse reads are stored in two separated files, you should call YAMP with the following instruction:

nextflow run YAMP.nf --reads1 QC_reads_fowards  --reads1 QC_reads_reverse --singleEnd false --mode characterisation

where QC_reads_fowards and QC_reads_reverse represent the paths to the raw data, and singleEnd is used to tell YAMP that you are providing two files in input.

In this case, YAMP will concatenate the two files in a single one that will be used for all subsequent analysis steps.

Please note that the command line may include further options, such as --prefix or --outdir.

Retro compatibility

The way YAMP handles externally QC'd reads 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.