Hi, I have a viral RNA-seq dataset that I am trying to run through ViReMa to look for deletion junctions. When I input my fastq files directly into ViReMa without trimming adapters first, my results look about how I would expect (multiple junctions returned with several reads each). However, when I trim adapters with cutadapt prior to running ViReMa, I get very few junctions returned, or (usually) no junctions at all.
Is it possible that adapter contamination would be causing artifactual junctions to be called? Or am I doing something super wrong in my trimming step and somehow removing information that ViReMa needs to proceed?
My cutadapt parameters look like this (just trimming Illumina universal adapters):
cutadapt -a AGATCGGAAGAG -o sample_cutadapt.fastq sample.fastq
And my ViReMa parameters looks like this:
python ViReMa.py --MicroInDel_Length 20 -DeDup --Defuzz 3 --Seed 25 --N 1 --X 2 --Output_Tag sample -ReadNamesEntry --p 6 bowtie1index/virus sample_cutadapt.fastq sample.results
I'm new to this type of analysis, so any help is appreciated.