ChromiumSingleCellPipeline

This repository contains scripts that can be used to produce files to operate the 10x Genomics Cell Ranger pipeline.

Usage

Reference preparation

References can be prepared using the instructions as detailed on the 10x Genomics website.

This repository includes nucFasta2GTF.py, which creates a GTF file based on FASTA sequences. This script makes two assumptions; first, the FASTA sequence represents the nucleotide sequence of a single feature, and two, the name of the gene is the same name used in the header of the FASTA sequence. The script will work on single and multiple FASTA sequences in a file.

Usage:

python2.7 nucFasta2GTF.py -i input_fasta.fa -o output_gtf.gtf

Generating PBS scripts

PBS scripts can be generated using the scRNASeqPipe.py script.

Usage:

python2.7 scRNAseqPipe.py --project ExampleProjectSheet.yaml --config pipeline_config.yaml

This script will generate PBS files for each stage of the pipeline. You may specify which stages to run in the project YAML file.

If you have any questions, feel free to email me at [email protected].