Schema for T2T Encode - T2T Encode Reanalysis
  Database: hs1    Primary Table: hub_567047_T2T_Encode_LOPeaks_HAP-1.H3K4me1 Data last updated: 2022-04-26
Big Bed File Download: /gbdb/hs1/encode/LO_peaks/HAP-1.H3K4me1.chm13v2.0.bb
Item Count: 114,439
The data is stored in the binary BigBed format.

Format description: Browser Extensible Data
fieldexampledescription
chromchr1Reference sequence chromosome or scaffold
chromStart166046118Start position in chromosome
chromEnd166049063End position in chromosome
field5HAP-1_H3K4me1.GRCh38p13_peak_6708Undocumented field
field6148Undocumented field
field7.Undocumented field
field83.92744Undocumented field
field917.8589Undocumented field
field1014.8815Undocumented field
field11842Undocumented field

Sample Rows
 
chromchromStartchromEndfield5field6field7field8field9field10field11
chr1166046118166049063HAP-1_H3K4me1.GRCh38p13_peak_6708148.3.9274417.858914.8815842
chr1166184429166185114HAP-1_H3K4me1.GRCh38p13_peak_670996.3.6523212.13429.61427194
chr1166186081166187710HAP-1_H3K4me1.GRCh38p13_peak_671096.3.7449412.18679.663841087
chr1166216106166216300HAP-1_H3K4me1.GRCh38p13_peak_671132.2.660975.136673.2509341
chr1166217032166217359HAP-1_H3K4me1.GRCh38p13_peak_671246.2.94076.658554.6195282
chr1166220706166221084HAP-1_H3K4me1.GRCh38p13_peak_671384.3.2869510.89298.48305205
chr1166222542166222917HAP-1_H3K4me1.GRCh38p13_peak_671478.3.1801310.19247.83938214
chr1166228789166229084HAP-1_H3K4me1.GRCh38p13_peak_671530.2.571414.943663.07764248
chr1166234428166234672HAP-1_H3K4me1.GRCh38p13_peak_671667.3.199248.999516.74816129
chr1166271436166272187HAP-1_H3K4me1.GRCh38p13_peak_671757.3.267767.937635.78028201

HAP-1 H3K4me1 hg38LO (hub_567047_T2T_Encode_LOPeaks_HAP-1_H3K4me1) Track Description
 

Description

These tracks represent a reanalysis of ENCODE data against the T2T chm13 genome. All ChIP-seq experiments with pair-end data and read lengths of 100bp or greater are included.

Track types include:

  • Coverage pileups of mapped and filtered reads
  • Enrichment of mapped reads relative to a control
  • ChIP-seq peaks as called by MACS2
  • ChIP-seq peaks as called by MACS2 in GRCh38 and lifted over to chm13

Methods

Prior to mapping, reads originating from a single library were combined. Reads were mapped with Bowtie2 (v2.4.1) as paired-end with the arguments "--no-discordant --no-mixed --very-sensitive --no-unal --omit-sec-seq --xeq --reorder". Alignments were filtered using SAMtools (v1.10) using the arguments "-F 1804 -f 2 -q 2" to remove unmapped or single end mapped reads and those with a mapping quality score less than 2. PCR duplicates were identified and removed with the Picard tools "mark duplicates" command (v2.22.1) and the arguments "VALIDATION_STRINGENCY=LENIENT ASSUME_SORT_ORDER=queryname REMOVE_DUPLICATES = true".

Alignments were then filtered for the presence of unique k-mers. Specifically, for each alignment, reference sequences aligned with template ends were compared to a database of minimum unique k-mer lengths. The size of the k-mers in the k-mer filtering step are dependent on the length of the mapped reference sequence. Alignments were discarded if no unique k-mers occurred in either end of the read. The minimum unique k-mer length database was generated using scripts found here. Alignments from replicates were then pooled.

Bigwig coverage tracks were created using deepTools bamCoverage (v3.4.3) with a bin size of 1bp and default for all other parameters. Enrichment tracks were created using deepTools bamCompare with a bin size of 50bp, a pseudo-count of 1, and excluding bins with zero counts in both target and control tracks.

Peak calls were made using MACS2 (v2.2.7.1) with default parameters and estimated genome sizes 3.03e9 and 2.79e9 for chm13 and GRCh38, respectively. GRCh38 peak calls were lifted over to chm13 using the UCSC liftOver utility, the chain file created by the T2T consortium, and the parameter "-minMatch=0.2".

Credits

Data were processed by Michael Sauria at Johns Hopkins University. For inquiries, please contact us at the following address: msauria@jhu.edu

References

Gershman A, Sauria MEG, Guitart X, Vollger MR, Hook PW, Hoyt SJ, Jain M, Shumate A, Razaghi R, Koren S, Altemose N, Caldas GV, Logsdon GA, Rhie A, Eichler EE, Schatz MC, O'Neill RJ, Phillippy AM, Miga KH, Timp W. Epigenetic patterns in a complete human genome. Science. 2022 Apr;376(6588):eabj5089. doi: 10.1126/science.abj5089. Epub 2022 Apr 1. PMID: 35357915.