GitHub - al-mcintyre/merip_reanalysis_scripts: Scripts for paper entitled "Limits in the detection of m6A changes using MeRIP/m6A-seq

Scripts for paper on MeRIP-seq reproducibility and detection of changes in m6A

BioRxiv preprint here.

This repository is for scripts to generate the figures. Bam files are too large to host here, but it is possible to download the fastqs from GEO/SRA and rerun alignment using STAR. Alternatively, run_full_analysis.sh provides a wrapper script to generate plots from saved results (requires all R packages and gtf files for mouse and human).

Please see R package DEQ to run DESeq2, edgeR, and QNB from input and IP bam files as described in our paper.

Name		Name	Last commit message	Last commit date
Latest commit History 9 Commits
anders_stress_2018/macs2_results		anders_stress_2018/macs2_results
barbieri_leukemia_2017/macs2_results		barbieri_leukemia_2017/macs2_results
batista_mettl3_2014		batista_mettl3_2014
bertero_smad23_2018/macs2_results		bertero_smad23_2018/macs2_results
chen_mirna_2015		chen_mirna_2015
dominissini_stresses_2012		dominissini_stresses_2012
engel_neuron_2018		engel_neuron_2018
fig3		fig3
fig4		fig4
fig5		fig5
fustin_circadian_2013/macs2_results		fustin_circadian_2013/macs2_results
geula_development_2015		geula_development_2015
hess_ftoko_2013/macs2_results		hess_ftoko_2013/macs2_results
hesser_kshv_2018/macs2_results		hesser_kshv_2018/macs2_results
huang_histonemeth_2019/macs2_results		huang_histonemeth_2019/macs2_results
huang_mettl14_2018		huang_mettl14_2018
li_leukemia_2017/macs2_results		li_leukemia_2017/macs2_results
li_ythdf2_2018/macs2_results		li_ythdf2_2018/macs2_results
lichinchi_hiv_2016		lichinchi_hiv_2016
lichinchi_zikv_2016		lichinchi_zikv_2016
lin_translation_2016		lin_translation_2016
liu_endometrialtumours_2018/macs2_results		liu_endometrialtumours_2018/macs2_results
meyer_original_2012		meyer_original_2012
neg_control_mocks		neg_control_mocks
rubio_hcmv_2018/macs2_results		rubio_hcmv_2018/macs2_results
schwartz_various_2014		schwartz_various_2014
tan_kshv_2018		tan_kshv_2018
tirumuru_hiv_2016		tirumuru_hiv_2016
wang_mettl314_2014		wang_mettl314_2014
wen_zc3h13_2018		wen_zc3h13_2018
winkler_hcmv_2018/macs2_results		winkler_hcmv_2018/macs2_results
xiao_fetaltissues_2019		xiao_fetaltissues_2019
yu_mettl3_2018		yu_mettl3_2018
zhang_alkbh5_2017/macs2_results		zhang_alkbh5_2017/macs2_results
zhou_heatshock_2015		zhou_heatshock_2015
README.md		README.md
exp_summary.txt		exp_summary.txt
get_most_highly_expressed.py		get_most_highly_expressed.py
merged_peak_analysis.sh		merged_peak_analysis.sh
plot_fig1a.sh		plot_fig1a.sh
plot_fig1a_counts_vs_expression.py		plot_fig1a_counts_vs_expression.py
plot_fig1a_summary.py		plot_fig1a_summary.py
plot_fig1b.R		plot_fig1b.R
plot_fig1bc.sh		plot_fig1bc.sh
plot_fig1c_replicate_overlap.py		plot_fig1c_replicate_overlap.py
plot_fig2.R		plot_fig2.R
plot_fig2.sh		plot_fig2.sh
plot_fig3.R		plot_fig3.R
plot_fig3_helper.R		plot_fig3_helper.R
plot_fig4.R		plot_fig4.R
plot_fig4_mergedpeaks.R		plot_fig4_mergedpeaks.R
plot_fig4prep.sh		plot_fig4prep.sh
plot_fig5.R		plot_fig5.R
plot_sfig1a.R		plot_sfig1a.R
plot_sfig1g.R		plot_sfig1g.R
plot_sfig2.R		plot_sfig2.R
plot_sfig2.sh		plot_sfig2.sh
rhelper.R		rhelper.R
run_full_analysis.sh		run_full_analysis.sh
run_kallisto.sh		run_kallisto.sh
run_macs2.2.sh		run_macs2.2.sh
run_metdiff_peakcaller.R		run_metdiff_peakcaller.R
run_star.1.sh		run_star.1.sh

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Scripts for paper on MeRIP-seq reproducibility and detection of changes in m6A

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