# v4 (11/29/2021)
- Updated TSS bed file for hg38 and mm10
  - hg38: https://www.encodeproject.org/files/ENCFF766FGL/@@download/ENCFF766FGL.bed.gz 
  - mm10: https://www.encodeproject.org/files/ENCFF454VOL/@@download/ENCFF454VOL.bed.gz 
- Use v4 as defaults for ATAC/ChIP
  - No difference for ChIP since it does not use the TSS bed
- Bug fix for v3 (TAB was falsely translated into SPACE). This bug affects test samples only.
  - hg38_chr19_chrM.dx.tsv
  - hg38_chr19_chrM.dx_azure.tsv
  - hg38_chr19_chrM.terra.tsv
  - mm10_chr19_chrM.dx.tsv
  - mm10_chr19_chrM.dx_azure.tsv
  - mm10_chr19_chrM.terra.tsv

# v3 (11/2/2021)
- Added genome TSVs for Terra to v3
  - hg38_chr19_chrM.terra.tsv
  - hg38.terra.tsv
  - mm10_chr19_chrM.terra.tsv
  - mm10.terra.tsv

# v4 (2/5/2021: not released yet)
- Updated hg38, mm10 only.
- New TSS files for hg38 and mm10.
  - Corrected wrong base.
  - hg38: https://www.encodeproject.org/files/ENCFF766FGL
  - mm10: https://www.encodeproject.org/files/ENCFF454VOL

# v3 (5/7/2020)
- Updated hg38, mm10 only.
- New blacklists (blacklist)
- New chromosome sizes file (chrsz)
- New annotation BED files (tss, prom, dnase, enh)

# v2
- For some reasons, v2 was not updated and it has been identical to v1.
- Let's not use v2.

# v1 and v2 (11/15/2019)
- Updated the following reference files (same contents but different md5sum) to match md5sum of gzipped files between portal and pipeline
  - hg38: `../hg38/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.gz`
  - mm10: `../mm10/mm10_no_alt_analysis_set_ENCODE.fasta.gz`

# v1 and v2 (10/20/2019)
- Added "regex_bfilt_peak_chr_name" to both v1 and v2

# v2 (10/18/2019)
- Renamed blacklist, bwa_idx and bowtie2_idx for hg38 and mm10.
  - These file names will have ENCFF prefix and md5sum hashes will be matched between pipeline and the ENCODE portal.
- Replaced TSS bed file for GENCODE v19 (hg38).
  - hg38/ataqc/hg38_gencode_tss_unique.bed.gz -> hg38/ataqc/tss.pc.gencode.v29.bed.gz

# v1 (2018)
- Initial genome database for ENCODE3.