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May 8, 2018, Tuesday

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Liya Wang edited this page May 8, 2018 · 1 revision
  • The EMS workflow
    • Documentation
    • EMS background
      • EMS induces only G-->A and C-->T mutation, do we need to filter out ins/del?
      • How to understand homozygous SNPs in the F2 results?
    • Yinping used bowtie2, old version of bcftools for snp calling and in-house perl script (keep index with regex), Zhenyuan used bwa, bcftools for calling and filtering
    • Verifications
      • Load in Genome browsers
        • bug in bwa_mem-0.7.17
        • need to create index for bcf
      • Check Yinping's paper? Which paper?
  • Nothing heard from Jawon
    • Andrew Olson called DMR from Andrew Smith's tools
  • Many versions of SciApps, use the maizecode version going forward
  • Circos plot for Sorghum data
    • Take bam file or other types of original file and we generate count data from a configuration file
    • Or we can generate circos needed file for each workflow
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