A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

What type of results are obtained in `dexseq_exon/counts/*.clean.count.txt`, are they normalized data? Or raw counts

Those are the output of `dexseq_count.py`, I think it just counts the reads overlapping exon parts, without any scaling/normalization.

Apology, when I run the command, I get only 4 folders as an output 1-contrastsheet, 2- Fastqc, 3- pipelineinfo 4- trimglore thats it, non of the results contains dexseq_counts

I am new to this workflow and please my apology in advance, but please be patience with me

What's you command line?  You'll need to specify tools, e.g. `--dexseq_exon`.

nextflow run nf-core/rnasplice --input /home/ahmed/data/mRNA_E_cig/samplesheet.csv --contrasts /home/ahmed/data/mRNA_E_cig/contrastsheet.csv --outdir /home/ahmed/nextflow --genome GRCm38 --skip_alignment --pseudo_aligner salmon -profile docker --max_memory 20.GB