This is a repository for higlass analysis
Cistrome DB data visualization flow:
- To do QC locally
- Gather bigwig data in iris(ssh -p 33001 [email protected]) server (optional)
- Transfer bigwig data and summit from iris server to kraken([email protected])
- Extract the chr22 data and conver them to bedfile with different resolution in kraken
- Extrate the chr peak position information and generate peak postion matrix in kraken
- Cluster all samples by peak position matrix and visulation in kraken or locally
- Select sample by cluster visulization result and generate seleted sample name file
- Generate whole genome bedfile and sorted it 8.1 Generate whole genomes bedfile with the specific resolution 8.2 Cluster selected samples again by peak_pos_chr22.csv and generate seleted sample name file with clustered order(Visulation)
- Sort samples order by new cluster labels in whole genomes bedfile (8.1)
- Transmit file from kraken to local folder(higlass-tmp)
- Generate mv5 data by higlass docker locally 11.1 open docker 11.2 conda activate higlassv2 11.3 higlass-manage start --version v0.6.17 11.4 clodius convert bedfile-to-multivec bedfile_16_20.csv --chromsizes-filename chromInfo.txt.allchr --starting-resolution 16 --num-rows 20 --row-infos-filename cluster_sample_name_20.txt
- Visulization 12.1 open docker 12.2 conda activate higlass 12.3 higlass-manage start --version v0.6.17 12.4 higlass-manage view --tracktype horizontal-multivec --datatype multivec --filetype multivec --position center --assembly hg38 --chromsizes-filename chromInfo.txt.allchr bedfile_200_sort.multires.mv5