GitHub - signalbash/strandedness_testing_scripts: Scripts for the how_are_we_stranded

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Name		Name	Last commit message	Last commit date
Latest commit History 10 Commits
simulated_data_scripts		simulated_data_scripts
.gitattributes		.gitattributes
README.txt		README.txt
annotate_studies_for_download.R		annotate_studies_for_download.R
arabidopsis_paired_end_pubs.txt		arabidopsis_paired_end_pubs.txt
arabidopsis_rnaseq.txt		arabidopsis_rnaseq.txt
get_paired_end_ENA_CURL.sh		get_paired_end_ENA_CURL.sh
hawsh_strandedness_results.txt		hawsh_strandedness_results.txt
human_figure_bioinformatics.R		human_figure_bioinformatics.R
human_paired_end_pubs.txt		human_paired_end_pubs.txt
human_rnaseq.txt		human_rnaseq.txt
intergenic_testing.sh		intergenic_testing.sh
make_intergenic_annotations.R		make_intergenic_annotations.R
make_plots.R		make_plots.R
paired_end_studies.R		paired_end_studies.R
run_hawsh.sh		run_hawsh.sh
trim_and_screen_yeast.sh		trim_and_screen_yeast.sh
yeast_fastqcscreen_summary.txt		yeast_fastqcscreen_summary.txt
yeast_filtered_results_summary.txt		yeast_filtered_results_summary.txt
yeast_intergenic_results_summary.txt		yeast_intergenic_results_summary.txt
yeast_paired_end_pubs.txt		yeast_paired_end_pubs.txt
yeast_rnaseq.txt		yeast_rnaseq.txt
yeast_trimmed_results_summary.txt		yeast_trimmed_results_summary.txt

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## R version 4.0.2 unless otherwise specified
## Note that some steps require manual annotation to proceed

# get 20 studies & make download scripts
./get_paired_end_ENA_CURL.sh
Rscript paired_end_studies.R
Rscript annotate_studies_for_download.R

#run hawsh on 1000 to 2000000 txs
./run_hawsh.sh

### YEAST ONLY ###
# fastqc/fastqscreen removal of reads mapping to other species/multimappers
./trim_and_screen_yeast.sh
## uses extract_paired_couples_yeast.R within script

# STAR alignment to genome + read counting to genes and intergenic regions/strand biases
./intergenic_testing.sh

# make plots
Rscript make_plots.R

See simulated_data_scripts/SIMULATION_README for information on how to run all simulation code & analysis