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CRG-CNAG / CalliNGS-NF

GATK RNA-Seq Variant Calling in Nextflow
Mozilla Public License 2.0
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Reading single end reads #19

Open Jokendo-collab opened 3 years ago

Jokendo-collab commented 3 years ago

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 commented 3 years ago

cc @lucacozzuto

Jokendo-collab commented 3 years ago

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 commented 3 years ago

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

Jokendo-collab commented 3 years ago

@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