Hi all! Glad to join and hoping to get a bit of help/advice here. I successfully ran the nf-core rnaseq pipeline after the fetchngs pipeline, pulling samples from SRA. These samples all failed the strandedness check, with about 15-24% sense, 65-70% antisense, and 15-20% undetermined (rather consistent per sample at these ratios). I set the samples to auto in the samplesheet, the smaples were then initially determined as reverse but the inference determined them as unstranded. I can attach the multiQC report if helpful, but based on what I read here: https://github.com/nf-core/rnaseq/pull/1306 it seems that these samples likely have genomic DNA or weren't processed well? They are form human patients, so more variation is expected, but I did not expect variation in strandedness. Is it possible to continue analysis on these samples for both differential expression and splicing changes? Or is that failure of strandedness enough to likely perturb the results such that any conclusion is meaningless? Thanks for any advice/help!!!

Hi, @Brian Amburn! Slack uses channels to organise discussions. Press the

...

more option on the left sidebar. Then hover over Your organisation, and finally select Channels to browse. Each nf-core pipeline has it’s own channel (e.g. #CE8SSJV3N). Please post any questions about specific pipelines in the relevant channel. If you’re not sure where to post your message, please ask @Rike Hanssen for help.