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alexdobin / STAR

RNA-seq aligner
MIT License
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--readFilesIn option is confusing #1506

Open pkhoueiry opened 2 years ago

pkhoueiry commented 2 years ago

On your README page, you mention that READ2 should be specified first and then read1. In the help page of STAR and other places, but also in the README, you give the example of READ1 then READ2: --readFilesIn read1.fq read2.fq.

alexdobin commented 2 years ago

Hi @pkhoueiry

what README pages you are referring to? --readFilesIn read1.fq read2.fq is the normal order. --readFilesIn read2.fq read1.fq is only used for the single-cell 10X 3' protocol.

Best, Alex

pkhoueiry commented 2 years ago

Hi @alexdobin,

In section "#barcode-and-cdna-on-the-same-mate", you used again read1.fq read2.fq. However you do mention below that it is a specific case.

All is clear now,

Thanks