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..

I don't see any pipeline parameters that directly control mismatches (or any aspect of the alignment). If you run the pipeline and look at the relevant processes in the table in the

execution_report_*.html

, there is column called

script

which shows the full command line of the tool used in the process (click on it to expand). If those tools have parameters specifying mismatches, you can see those, and if not, you know that the defaults were used. If you wanted to add/modify parameters used by the tools, you could do that by modifying

ext.args

in a config file.

okay thanks very much @Thomas Danhorn, ill check that file to see the command line output. i believe was able to find the command in the modules and it seems that there isn't any parameter in the bowtie command to limit mismatches, but they dont seem to ever exist in the reads to the mature miRNA, which is partly what im trying to reconcile

I is likely that the defaults are being used, so you can look at the bowtie docs to find what those are.

yep thats what it looks like, just suprised that there are no mismatches found in tghe mature mappings with those parameters

You could look at the unmapped reads if you are worried something was wrongly rejected.

yes good point i will do that