mapping with 5' R2 only data

alexdobin / STAR

RNA-seq aligner

MIT License

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mapping with 5' R2 only data #1704

Open echothefox opened 2 years ago

echothefox commented 2 years ago

Hi, I got some data generated from 5' R2 only chemistry. I think I don't have pair-end reads and the majority of information are stored in R2.fastq file. In this case, should I use: readFilesIn R1.fq R2.fq ?

alexdobin commented 2 years ago

Hi @echothefox

the read-end containing cDNA sequence should go first, and the read-end that contains the barcode should go 2nd.