NEP Deep mutation scanning and IAV RNA species(mRNA/cRNA/vRNA) quantification

Dependencies

• python=3.6
• snakemake
• flash
• seqtk
• cutadapt
• STAR
• pysam

Installation

Install everything dependencies by conda:

conda create -n NEP -c bioconda -c anaconda python=3.6 seqtk flash

Before running the analysis, do:

source activate NEP

DMS analysis

1. set the env
2. Run analysis:
   • go into /script/ folder
   • set the PROJECT_PATH variable in nep_pipeline.smk file accordingly
   • do: snakemake --use-conda --cores 4 -s nep_pipeline.smk -j 2 to excute the analysis

IAV RNA species analysis

1.1 Make reference

RNAseq_script/make_ref.sh

1.2 Align to IAV genome by STAR

RNAseq_script/pipeline_align.sh

1.3 RNA quantification (htseq-count)

RNAseq_script/pipeline_count.smk
python RNAseq_script/align2count.py