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MonashBioinformaticsPlatform / RNAsik-pipe

RNAsik - more than just a pipeline
https://monashbioinformaticsplatform.github.io/RNAsik-pipe/
Apache License 2.0
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Ability to explicitly specify pairs #45

Open pansapiens opened 5 years ago

pansapiens commented 5 years ago

As an alternative to using the -pairids option, RNAsik should allow pairs to be explicitly indicated, eg via a CSV/TSV file like (sample_name, R1, R2):

wildtype, myreads_R1_001.fastq.gz, myreads_R2_001.fastq.gz
mutant, SRA00001_1.fastq.gz, SRA00001_2.fastq.gz

This should probably just replace sampleSheet.txt, since it could serve the same purpose. -pairids can remain, but would be ignored/throw an error when a sample sheet is provided.