scseq

This repository contains scripts and tools for single cell RNAseq, as initially developed by Dominic Grün and Alexander van Oudenaarden at the Hubrecht Institute, Utrecht, The Netherlands.

This code has moved to https://bitbucket.org/princessmaximacenter/scseq/ . Contact me if you want access.

It contains (often heavily modified) code from other people, specifically from Dominic Grün (now at MPI Freiburg), Lennart Kester and Abel Vertesy. For related code, see Abel Vertesy's repository, in particular the Python/MapAndGo and Python/Concatenator subdirectories

Contents

General stuff

• env.sh.example - sets PATH en PERLLIB so they don't have to be hard-coded
• tools.pm - functions used by the perl scripts

barcodes and external controls

• holstegelab_EC.fa - kept for historic reasons
• ERCC92.fa - superset of holstegelab_EC.fa, well-known set of external spike-in controls
• cel-seq96_barcodes.csv - initial set of barcodes
• celseq2_bc384.csv - barcodes used for celseq2, 384-well protocols

preparing the reference transcriptome

• mask_polyA.pl - masks any /A{10,}/ in reference transcriptome
• ucsc2gtf.pl - converts UCSC RefSeq.txt table to a gtf file
• polyXY.pl - finds stretches of e.g. AAAAAAAAGGGGGGGG etc.
• merge_isoforms_gtf.pl - creates 'supertranscripts', i.e. (virtual) transcripts consisting of all possible exons

mapping and postprocessing

• do_mappings_strand_cs2v2.pl - driver script for preprocssing, mapping and bookkeeping. See also Abel Vertesy's Python/MapAndGo/MapAndGo.py in https://github.com/vertesy/TheCorvinas
• add_bc_to_R2.pl - preprocesses the reads prior to mapping.
• process_sam_cel384v2.pl - bookkeeping and statistics per cell. Needs code from https://github.com/plijnzaad/demultiplex for recovering mismatched cell barcodes