short_insert_search_in_amplicon

This repo is created for a custom analysis which involves sequencing target sequence which are very short (11-23bp long) being amplified by a set of primers from the system of interest (bacteria culture) and finding the expression level of the sequence of interest. HOW TO USE

1. Install miniconda/anaconda
2. Create conda environment with yaml file
   • conda env create --file environment.yml
3. Change directory to work directory
   • cd /mnt/volume1/
4. Ensure data is found inside fastq folder ie /mnt/volume1/fastq
5. Run nextflow script
   • nextflow run custom_trimFASTP_mapPYTHON.nf -resume --outdir results -with-report log.html