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.
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.