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How to run YAMP with QC'ed reads
Alessia edited this page Jul 10, 2017
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This tutorial aims at explaining how to run YAMP using reads that have externally QC'ed.
To use YAMP with externally QC'ed sequences you need to create a file structure that is compatible with the one created by YAMP. To do so, you should:
- create a folder called
outputdir/mysample
whereoutputdir
is the directory where the results will be stored andmysample
is a prefix that will be used to label all the resulting files (as explained in the How to run YAMP tutorial). These two parameters will be used also tu run YAMP. - (if needed,) collapse the QC'ed files in a single FASTQ file that should be saved in the
outputdir/mysample
asmysample_clean.fq
. If you have paired-end QC'ed reads you can use the following command:
bbmerge.sh in1=read1.fq in2=read2.fq out=mysample_clean.fq
We can now run YAMP with the following command:
nextflow run YAMP.nf --prefix mysample --outdir outputdir --mode characterisation
where mysample
and outputdir
are those used in the step above
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