RNAseq Pipeline to qc RNAseq FASTQ files with options for trimming, assembly, and export to iDEP/DEBrowser ready input.

This script accepts untrimmed FASTQ files and performs the following:

• Quality and adapter trimming using Trimmomatic
• Transcript abundance quantification using Kallisto
• Alignment and quantification to Human mitochondrial, and ribosomal sequences (5.8s, 18s, 28s) using Bowtie2
• Generate FASTQC output
• Returns a csv with read counts of the original FASTQ file, reads aligning to the ribosome and mitochondrial sequences, and mapped reads to the Human transcriptome.

All paired end FASTQ files in the folder with the python script will be run through the pipeline. Wildcard searches are used to distinguish R1 and R2 files, so they must have "R1" and "R2" in their filenames. Trimmomatic, Bowtie2, Kallisto, and SPADES must be installed and added to $PATH. The python script pulls from NCBI and the bin folder located inside this repo. As a result internet access is required to run this script. DEBrowser must be installed in your default R environment as well.

The required reference sequences for the Bowtie2 alignment and adapters.fa for the trimming will be automatically downloaded and built by the script. The only file that must be provided is for the optional kallisto alignment: Transcriptome.idx.

• --paired <True/False> Default: Single
• --trimmomatic "< Any Trimmomatic options to be entered after the 'trimmomatic PE' command>"
• --kallisto "<Any Kallisto options to be entered following 'kallisto quant'>"
• --Debrowser <True/False>
• --fastqc <True/False>
• --spades <True/False>

python3 slowqc.py --paired True --trimmomatic "-phred33 -threads 8 ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:75" --kallisto "-i ~/bin/homo_sapiens/transcriptome.idx --threads 8" --debrowser True --spades True