Tutorial (Under construction)

    Workflow
  • Registration -> New Submission (dashboard) -> Annotation & File-uploading (edit) -> Further Analyses (analysis)
  • How to get an account
    • fill the form -> email-based communication -> completed
    • dashboard for each user is now available
    • "New Submission" available now. Wysihtml implemented
  • How to upload and control files
    • Keywords
    • one-click uploader -> MySQL designed for add&del -> sharing with others
    • acceptable file formats : WEBM, MP4, PNG, JPEG, JPG, PDF, ZIP, BZIP, TAR, GZ, BED, GTF, TXT, BAM, HIC
    • One-uploading for setting (json or xml, excel) not yet
  • How to anlaysis
      • ".hic" file
    1. Creating a Genome Browser track
    2. Converting hic to mcool (hic2cool)
    3. Balancing mcool (cooler)
    4. Generating cooler.tree (cooler)
    5. Retrieving KR/SCALE/VC/...etc file (hicConvertFormat)
    • NGS: JBrowse2 features .. completed (so far, for RNA-seq BAM, WGS BAM, HiC)
    • HiCExplorer installed (link)
    • Juicer & Juicer tools installed
    • Hi-C modeling: PHi-C2 installed (github)
      • .hic -> .mcool by hic2tool -> attrs&tree by cooler
      • GUI designed
      • Viewer???
    • Video: mp4 converted to "webm" by ffmpeg
    • JBrowse2@YouTube: [here]
    • BAM filesize should be reduced
      • %>samtools view -F 4 input.bam -ob output.bam -@ 4
      • CRAM file reduces the BAM filesize (~50%)
        1. %>samtools faidx genome_hg38.fa
        2. %>samtools view -F 4 -C -T genome_hg38.fa input.bam -o output.cram
        3. %>samtools sort output.cram -O cram -o output.sorted.cram
      • Index file will be created.
        • %>samtools index output.sorted.bamORcram
      • BigWig file will be created from the BAM or CRAM file.
        • %>bamCoverage -of bigwig --samFlagExclude 4 --bam input.bamOR.cram -o output.bw
          • /ul>