Hiya!! My question pertains to the nf-core/smrnaseq pipeline. The smrnaseq libraries I am processing through this pipeline had their libraries prepared using the 'Takara SMARTer smRNA-Seq Kit for Illumina' that does not use UMIs. They also suggest in their manual (Pg 13) how to trim the reads using cutadapt (cutadapt -m 15 -u 3 -a AAAAAAAAAA input.fastq > output.fastq). Should I still set my profile option as "_-profile_ singularity,illumina", or should I just set it as "_-profile_ singularity" and set _--trim_fastq_ false and feed the pipeline with trimmed reads to begin with? My sequencing is PE 151bp.

I recommend trying #CL66GAJBF as you might get a better response there