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