Standard RNA-seq snakemake pipeline.
The test data is not part of this repository and needs to be downloaded separately here:
wget ...
To clone into the pipeline type
git clone git@github.com:fischuu/Snakebite-RNAseq.git
The pipeline is configured in the file ... with the following required parameters.
In addition, the follwoing must be provided
cut -d'-' -f1 samples > animal cut -d'-' -f2 samples > pathogen cut -d'-' -f3 samples > time cut -d'-' -f4 samples > replicate cut -d'-' -f5 samples > sequencer
paste -d'\t' samples animal pathogen time replicate sequencer > sampleList.tmp
rm animal rm time rm sequencer rm pathogen rm replicate
printf "sample\tanimal\tpathogen\ttime\treplicate\tsequencer\n" > header cat header sampleList.tmp > sampleInfo.txt rm sampleList.tmp rm header
Under development and possible not yet stable for production