Prim-5, Skarmeta_Lab, DCD003075SQ (hub_280355_DCD003075SQ_DCD018723DT_signal)
  Position: chr10:33,840,892-34,129,251
Total Bases in view: 288,360
Statistics on: 16,993 items covering 288,360 bases (100.00% coverage)
Average item spans 16.97 bases. Minimum span 1 maximum span 6,804
Average value 0.189748 min 0 max 3.15878 standard deviation 0.388072
View table schema

Go to ATAC-seq tracks track controls

Data last updated at UCSC: 2019-02-27 06:51:16

ATAC-seq tracks

The whole ATAC-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=ATAC-seq-assay_type)

This is an ATAC-seq super track that groups together signal of ATAC-seq data (bigWig format) together with the narrow peak signal (bigNarrowPeak format). regions (bigBed format).

The ATAC-seq pipeline used in the analysis is an adapted ATAC-Seq / DNase-Seq Pipeline developed at Kundaje lab (https://github.com/kundajelab/atac_dnase_pipelines). The pipeline consists of the following steps:

  • Quality filtering and trimming of raw reads (Trim-galore)
  • Mapping reads to the reference genome (Bowtie2)
  • Filtering of reads in the output bam file (samtools and sambamba)
  • Marking optical duplicates (Picard tools)
  • Deduplication (samtools and sambamba)
  • Format conversion to a more manageable tagAlign format (https://genome.ucsc.edu/FAQ/FAQformat.html#format15)
  • Tn5 shifting of aligned reads
  • Peak calling (Macs2)

The analysis also include fragment length distribution of aligned read pairs, which allows separation of reads into nucleosome-free region spanning, mononucleosome spanning, and di and more nucleosome spanning.

Track definition: ATAC-seq tracks consist of 2 parts: #. ATAC-seq signal. #. Narrow peak signals.

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