10:15a – 10:00p
- prepare slides for chat with Levine
- Reply to SW
Mi Seq analysis of off target hybridization sequence bias
- New strategy:
- Generate new fasta file with the entry ID number as the first 5 digits (00000 – 99999).
- num2str this and use that to pull out the sequence entry from the loaded fasta file.
- now we have the reference sequence and the read sequence without any massive strfind calls.
mRNA read alignments
- installed FCIV (microsoft’s checksum tool).
- ran on rep1 BAM data
- Attempted running cufflinks on Tubigen Galaxy browser following successful upload of BAM file.
- Tubigen Galaxy gives error cufflinks not found ?
- Did not have genome specified or reference gtf file uploaded. Uploading now.
- All modules in RC example are many versions out of date.
- RC computing is
Planning next round of probe sequencing
- 8 sublibraries, 2x PCR -> prep for sequencing with single round PCR addition of adapters
- prep each of 8 sublibraries to make probes, T7 reaction, RT reaction (with cy3 primer)?, oligo-cleanup
- prep the probes for sequencing with single round PCR adapter additions
- passage cells.
- both new flasks look good. Density substantially higher on original flask, let’s split this one again tomorrow.
- running diff-binding model for PhM conc effects (instead of capping model)
- Making slides for chat with ML
- started presentation on GoogleDocs using the last update for Ting Wu and the SDB slides as a stub.
- working on getting more clearly contrasted images of chromatin domains for slides
- analyzed AbdA (twice, overwrote data with D11)
- analyzed D11 data
STORM to image / re-image
- E10rna (focus lost?)
- E01 (focus lost?)