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This stores scripts used to attempt to reproduce the data on yeastepigenome.org via chexmix, and scripts used to re-call peaks with macs3

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NameName
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chexmix_input
chexmix_input
 
 
chexmix_output
chexmix_output
 
 
exclude_regions
exclude_regions
 
 
LICENSE
LICENSE
 
 
README.md
README.md
 
 
annotatePeaks_array.sh
annotatePeaks_array.sh
 
 
chexmix_array.sh
chexmix_array.sh
 
 
chexmix_designs.txt
chexmix_designs.txt
 
 
chipexo_run_accessions.tsv
chipexo_run_accessions.tsv
 
 
convert_gtf_chr_names.sh
convert_gtf_chr_names.sh
 
 
convert_gtf_chrnames.awk
convert_gtf_chrnames.awk
 
 
convert_names_gtf.sh
convert_names_gtf.sh
 
 
download_chipexo.sh
download_chipexo.sh
 
 
fetch_yep_peaks.sh
fetch_yep_peaks.sh
 
 
macs3_array.sh
macs3_array.sh
 
 
rename_genome.sh
rename_genome.sh
 
 
sacCer3.ensGene.gtf
sacCer3.ensGene.gtf
 
 
sacCer3.ensGene_chr_numeric.gtf
sacCer3.ensGene_chr_numeric.gtf
 
 
sacCer3.info
sacCer3.info
 
 
sacCer3_cegr.fa
sacCer3_cegr.fa
 
 
sacCer3_genes_as_exons.gff
sacCer3_genes_as_exons.gff
 
 
yeast.back
yeast.back
 
 

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rossi_chipexo_peak_calling

This stores scripts that I used to attempt to recreate the peak calls in yeastepigenome from the bams shared there, and chexmix. That consistently failed.

I instead used macs3 to re-call peaks, and those scripts are here also

About

This stores scripts used to attempt to reproduce the data on yeastepigenome.org via chexmix, and scripts used to re-call peaks with macs3

Resources

Readme
MIT license
Activity
Custom properties

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Report repository

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