Pipeline for aligning RNA-seq data from plasmidsaurus

conda create -n paramecium_align \
    bowtie2 \
    samtools \
    fastqc \
    multiqc \
    subread \
    r-base \
    -c bioconda -c conda-forge -y

conda activate paramecium_align

chmod +x align_paramecium_single_end.sh

./align_paramecium_single_end.sh \
     sample1.fastq.gz \
     sample2.fastq.gz \
     sample3.fastq.gz

or:

chmod +x align_paramecium_single_end.sh
./align_paramecium_single_end.sh *.fastq.gz

Output in the end will be:

paramecium_gene_counts.txt