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.
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
Two of the scripts are useful also without the complete pipeline.
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.
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.
General: bowtie2, python2.7 Python packages: HTSeq