A snakemake pipeline for identification of extreme reads pile-up sites across genome from 10x Genomics single cell RNA-Seq experiment.

Installation

• Step 1: install miniconda3 (Download). For MacOS:

$ sh Miniconda3-latest-MacOSX-x86_64.sh

• Step 2: install snakemake

$ conda install -c conda-forge -c bioconda snakemake=5.11.2

Check snakemake installed successfully

$ which snakemake && snakemake --version

if you didn't see snakemake in your path, you may close and re-open your terminal to activate the effects, and check again.

• Step 3: download and run

$ git clone https://github.com/yh154/Pyup.git

$ cd Pyup

$ snakemake --cores 1 --use-conda -s Snakefile

Input and Output

All inputs and parameters are controlled by config.yaml. Using a text editor to indicate input bam, chromosomes of interests, pileup site width and et al.

The pipeline expects a single bam file from 10x Genomics RNA-Seq experiment and identify chromosome-wise pileups.

The outputs of the pipeline contain a single 'Pyup.output.txt' of identified extreme pileup regions and quantification details for each chromosome.

Note: the chromesomal names should be the same as in the header of bam, i.e. "chr1" is different from "1".

Dependencies

The pipeline is dependent on conda3, snakemake, python3, bamtools, samtools, umi_tools