Saturday 07/28/12

10:30 A -2:00P, 4:30P-7:30P, 9:50P-11:00P

  • Finish O/N confocal of m197.  Imaging plane too high, lower sections of most embryos not fully imaged.  Set up rescan. ~10:30A.
  • working on parsing genomic data to test changes in H3K27me3 occupancy in A8 using Esc mutant embryos fully converted to A8 (maternal and zygotic nulls).
  • Troubleshooting parsing.
  • final approach, detailed manipulations in Galaxy with added tool QSEQ to FASTQ:
  • Cutting appropriate columns (c1:10,+c22)  that match illumina qseq format
  • Using Tuebingen Galaxy instance (not space limited) to process H3K27 data from Esc for analysis.
  • ‘Other Tools’, ‘Filter and Sort’:  ‘Filter’ lines with column value: c11==Y
  • ‘Text Manipulation’ Add column, value =1.  Then’Cut’ lines 1-10 + 12
  • Then QSEQ to FASTQ.
  • Then FASTQ groomer.  with Sanger (QSEQ to FASTQ gives a file that thinks its FASTQ format).
  •  Now have properly formated FASTQ file, can run Illumina Bowtie, SAM to BAM, and view in USCS genome browser.  Should also be able to Boxplot quality statistics.
  • Received browser tracks from Chopra/Hendrix Mol Cell paper from Dave
  • Confocal of slide m197 rpt


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