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.