This repository contains the directory structure, scripts and metadata used to run dynast on sequencing pilots and experiments for:
Deep dynamical modelling of developmental trajectories with temporal transcriptomics Rory J. Maizels, Daniel M. Snell, James Briscoe
To re-run:
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fastqs must first be downloaded from GEO (GSE236520), and scripts must be updated to reflect the new position.
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the STAR directory must be populated with reference genome files (specifically, something that looks like
Mus_musculus.GRCm39.104.gtf.gzandMus_musculus.GRCm39.dna_sm.primary_assembly.fa) with the GTF and IDX variables of scripts updated to reflect this change. -
Each experiment's processing script, "scifate_*.sh" can then be run. Excel sheets in the metadata should relate particular fastq files to particular experiments and conditions; so be sure not to change the name of any fastqs. Analysis was run using the environment detailed in sci_processing.yaml with dynast version 1.0.1.
Any problems? email [email protected]