Overview

This is a pipeline for the CEL-Seq method. CEL-Seq is a HTS method published hashimshony et. al(2012), based on RNAseq. It typcially reads only the 3'UTR end of mRNA transcripts and is stranded.

The pipeline input is paired-end read files (FASTQ format,) alongside a reference genome and annotation and outputs a read count.

Complete workflow

To use the pipeline completely, you need to create a config file (use the config_file_example.txt as an example). The config file tells the pipeline what are the required actions on which files, and references the references.

The invocation is:

pijpleiding config_file.txt

Useful scripts

Two of the scripts are useful also without the complete pipeline.

bc_demultiplex

A CELSeq demultiplexer, to demultiplex the CELSeq barcodes. It also saves UMI information with the reads.

Use bc_demultiplex --help to understand the input format.

htseq_count_umified

An adapation of the htseq_count script from the HTSeq package, to count each UMI only once, based on the UMI information from bc_demultiplex.

Dependencies

General: bowtie2, python2.7 Python packages: HTSeq