not sure if this is the best place to put this, but ive been trying to understand some of the paranmeters used the the smrnaseq pipeline https://github.com/nf-core/smrnaseq/tree/master. specifically I'm trying to understand how many mismatches are allowed during mature miRNA and hairpin alignment, so I can understand if reads with A/U tailing will be alignmed (mainly in the hairpin context). my understanding was that no mismatches were generally allowed for at least the mature mirna mapping to avoid cross mapping to similar miRNAs, but looking at the bowtie command specification it doesnt seem like any specific parameters to limit mismatches are used in the mature or hairpin mapping. looking at the reads from the mature mapping in IGV however, I dont really ever see any mismatching bases.. hoping someone might be able to help me understand..

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

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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 @James Fellows Yates for help.

#CL66GAJBF is the best place to ask, ifyou've not already?

ah and just a quick hint that it does not make so much sense to repeat the same question across multiple channels 🙂 people are eager to help but finding the right place to ask is the best way to get a quick answer

ah ok thanks. i can remove from the other channels. it is posted on smrnaseq now