Currently in our lab we are making an effort in order to find important regulatory regions in breast cancer cells. So, for that purpose we had sequenced DNA I hypersensitive fragments without replicates at different time points of single-ended 18bp each read.
I can summarize that in DNase-seq the workflow goes like:
- Lab work/Sequecing
- Quality control check/read trimming
- Mapping to reference genome (BWA or bowtie)
- Identification of regions with signal
- Differential signal enrichment between conditions
- Motif analysis of TF and Histone marks enrichment
- Further specific analysis
The first question is which is your general pipeline? Is it more or less like I show?
Also, I have seen that there not many softwares/pipelines developed to analyze DNase-seq data for signal enrichment:
- F-seq (ChIP-seq and Dnase-seq) : http://fureylab.web.unc.edu/software/fseq/
- HotSpot (ChIP-seq and Dnase-seq) : http://www.uwencode.org/proj/hotspot-ptih/
- MACS (I'm not sure if it's really a good choice, but saw some papers using it) : http://liulab.dfci.harvard.edu/MACS/
I was planning to use F-seq because I found clearly enough to proceed, but as far as I know F-seq doesn't compute any significance test to rank regions. So, at this point how you assess region significance?
Thanks for your support and help!