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.