This generalized pipeline will take user defined raw paired-end fastq files from illumina and run the following programs.
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Run fastqc quality control check of each sample
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Index the user defined transcript assembly using salmon
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Generate pseudocounts from the .fastq files using the salmon index
This pipeline requires fastqc and salmon. I recommend the use of conda environments to install these packages, following these instructions for installation of miniconda.
To create the enviornment, run the following command:
conda create -n rnaseq -c conda-forge -c bioconda fastqc salmon
To activate this enviornment:
conda activate rnaseq
In order to use this pipeline, the user needs to supply a transcriptome file. Furthermore, illumina paired-end sequencing reads should have the standard _R1_ & _R2_ file naming convention.
To run the pipline, run the following command
bash rna_seq_pipeline.sh
-s <path/to/sequence/directory>
-o <path/to/output/directory>
-a <path/to/assembly/file>
-t <number of threads>