10:30 A – 7:00P
Working on presentation
Check split cells.
- S2R+ ~80% confluent, should be able to split tonight.
- Kc167 < 50% attached
Genome browser
- Tubigen version of Galaxy not talking to UCSC. Spent several hours troubleshooting workflow only to find this. Previous saved BAM set does display just fine from the PSU Galaxy server (which is 50 times slower … 🙁 ).
- Setting up workflow to convert misformatted Illumina qseq files to usable BAM/BED files.
- Still need to use Tubigen to do the initial steps. Basic workflow and mapping to get into SAM format is 20 GB +, which is more space than allowed on PSU galaxy (4GB max).
- Final SAM files are much smaller (~250 Mb), which can with multiple tries be successfully downloaded without network error interruptions.
- Display issues with BAM BED files — would like averaged read density corrected by the input lane, rather than a direct image of all mapped reads…