H3K4me3, Prim-5, Mueller_lab, nan (hub_280355_H3K4me3_DCD001525SQ_DCD009064DT__signal)
  Position: chr10:33,840,892-34,129,251
Total Bases in view: 288,360
Statistics on: 7,314 items covering 288,360 bases (100.00% coverage)
Average item spans 39.43 bases. Minimum span 1 maximum span 19,754
Average value 0.917611 min 0 max 45.376 standard deviation 3.64229
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Go to ChIP-seq tracks track controls

Data last updated at UCSC: 2018-06-01 07:07:48

ChIP-seq tracks

The whole ChIP-seq dataset including raw data and metadata annotation can be found in the DANIO-CODE Data Coordination Center (https://danio-code.zfin.org/dataExport/?view=table&selected_facet=ChIP-seq-assay_type)

This is a ChIP-seq super track that groups together signal (bigWig format) and narrow peaks (bigNarrowPeak format) of ChIP-seq data. regions (bigBed format).

The ChIP-seq pipeline used to generate these tracks are described https://gitlab.com/danio-code/DANIO-CODE_ChIP-seq.

Briefly, the pipeline consists of:
  1. Aligning reads (bwa): Aligning raw reads to the reference genome.
  2. Filtering of aligned reads: Filtering the ba file for unaligned reads and and duplicates with samtools and sambamba.
  3. Optical duplicates detection: Detect optical duplicates with Picard tools.
  4. Duplicates removal: Second round of filtering with samtools and sambamba.
  5. Cross-correlation analysis.

Track definition: ChIP-seq tracks consist of 2 different types: #. ChIP-seq signals. #. ChIP-seq narrow peaks.

For more information on how the data were processed, please refer https://gitlab.com/danio-code/ADANIO-CODE_RNA-seq.