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