The whole CAGE-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=CAGE-seq-assay_type)
This is a CAGE-seq super track that groups together signal (bigWig format) and
tag cluster regions (bigBed format). These tracks were produced by the DANIO-CODE CAGE-seq pipeline.
- The main processing pipeline of the DCC ("CAGE_pipeline_v1.6") consists of 4 different processing steps :
- #.Sequence quality filtering / trimming (FastQC)
#.Mapping to the reference genome (Bowtie)
#.Tag clustering (Paraclu-9)
There is also an additional signal conversion step for reformatting the input from the main pipeline
to adequate UCSC track input format (DANIO-CODE CAGE-seq signal conversion pipeline v1.0).
CAGE-seq tracks consist of 2 parts:
#. CAGE-seq TSS signals
#. and CAGE-seq tag clusters
For more information on how the data were processed, please refer https://gitlab.com/da-bar/DANIO-CODE_CAGE-seq.