March 13, 2018, Tuesday

• Cancelled
• Possible improvements to the ENCODE RNA-Seq workflow
  • Add checking for unzipped reads to STAR_align_Stampede2 (or bzipped, ignore for now)
  • Add code to generate index files for STAR_align_Stampede2
    • For alignments to both genome and transcript? (yes done)
  • Add output-genome-bam option to RSEM_quant for alignments in either genomic or transcript coordinates (ignore)
  • STAR index may fail if 100 GB storage is not guaranteed
    • Consider moving to Wrangler? How about their queue
• Possible improvements to the GWAS workflow
  • Move apps to TACC?
  • Compress marker results
• Tutorial
  • Visualization for strand-specific reads or not: https://galaxyproject.org/tutorials/rb_rnaseq/stranded_result.png
  • Visualization for all reads being derived from forward or reverse strand (needed by RSEM_quant)
• Basic flow for visualization
  • Click on file to go to Data Common landing page
  • Open in Discovery Environment
  • Generate Genome Browser link
  • Visualize in Genome Browser (JBrowse? Dalliance? UCSC? Apollo? Hosted on data.maizecode.org?)
  • https://github.com/Arabidopsis-Information-Portal/jbrowse-tabix-howto/wiki/Steps-to-process-BAM-files
    • This is for TAIR10 only
  • https://data.sciapps.org/view2/
    • Shall we set up all MaizeCode genomes plus Sorghum genome? Or all plant genomes?