GM Suite Flyer

Intro. 1

Intro. 2

Tutorial (Under construction)

  • 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, JPG, PDF, ZIP, BZ, TAR, GZ, BED, BIGBED, BIGWIG, TXT, BAM, CRAM, HIC, MCOOL, PDB, CIF, RDATA, RDS
      • 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
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