Unpaired Reads

[AnkeKloock]

How do I analyze unpaired reads? I have paired reads for my own RNAseq study, but for the ones from other studies I only have unpaired reads. Is there a way to analyze these with SeqNSlide?

[igordot]

You can use either paired or unpaired reads. When you run sns/gather-fastqs, files will be added to the samples.fastq-raw.csv file. The first column is the sample name, the second column is the R1 FASTQ, and the third column is the R2 FASTQ (if available). Each line contains a single FASTQ (or a pair of FASTQs for paired-end experiments).