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A pipeline for quantifying and exploring transposable element expression
Developed by Peter A. Stockwell and Chiemi F. Lynch-Sutherland. Department of Pathology, Otago Medical School, University of Otago, Dunedin, New Zealand.
README.md - this file
RepExpress_processing.pdf - documentation.
Scripts - containing Main processing scripts:
generate_combine_gtfs.sh - to build STAR index and build required GTFs
map_count_reads.sh - run STAR, featureCounts & stringtie on each sample
compare_express.sh - combine expression counts for a series of similar samples
contrast_express.sh - take combined expression counts for two different series of samples
run_deseq2.sh - differential gene expression by Bioconductor DESeq2 analysis
Example_scripts - example parameter files showing the required parameters for each process.
Readme.txt - a description of each example parameter file
basic_params.sh - system-specific details required for all other processing
map_params.sh - mapping details for map_count_reads.sh execution
combine_params.sh - details for the compare_express.sh run
genloc_file_list.txt - file with names of genloc files needed for compare_express.sh
contrast_params.sh - details for the contrast_express.sh run
deseq2_params.sh - details for DESeq2 running with run_deseq2.sh
brain_tpm_list.txt & testis_tpm_list.txt - lists of TPM featureCounts files for deseq2_parameters
Installation:
Scripts in the Scripts directory can either be copied into your current working directory or some other appropriate place. The documentation in RepExpress_processing.pdf assumes the former. It may necessary to make the scripts executable by
chmod a+x *.sh
======= A pipeline for quantifying and exploring transposable element expression
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