Reading single end reads

[Jokendo-collab]

Hi,

I have a single end reads and I would like to use this powerful pipeline to process my samples. Which command can I use to process this type of data since I can see the pipeline only accepts paired end reads.

[pditommaso]

cc @lucacozzuto

[Jokendo-collab]

cc @lucacozzuto I am trying to analyze single end RNAseq data and the pipeline is designed to take up paired end reads. Could show me how I can single end reads as input?

[laurahspencer]

I'm also interested in running this pipeline with single end reads

[Jokendo-collab]

@laurahspencer this tool is a great tool but it's yet to be configured to accept single end read, @pditommaso can help in sorting this