Meeta Mistry

add --validateMappings to salmon command

1

this is now running by default in bcbio, we should incorporate it with an explanation why. Also Rory says: "Also, I’ve been turning on quantitate_genome_alignments which uses the STAR alignments...

The DGE lessons have a better explanation - we should incorporate this https://github.com/hbctraining/DGE_workshop_salmon/blob/master/lessons/01_DGE_setup_and_overview.md

instead of moving the results to the new folder, have it go there automatically. we do it in automation anyway

MultiQC accesses the aux folder to report fragment length distribution, wondering if it also would report information if we had added bias correction parameters (results are also in the aux...

update the module

1

the downloading_from_SRA.md lesson needs to be updated. The code as is doesn't work. One issue was resolved using current module `module load sratoolkit/3.0.2`

zoom poll questions to assess self-learning

2

by having these questions, we avoid spending too much time going through the individual lessons and have time for in-class exercises

Once you have run: ``` # Filter out low quality cells using selected thresholds - these will change with experiment filtered_seurat = 500) & (nGene >= 250) & (log10GenesPerUMI >...

Update code and associated images in the scRNA-seq repo ; specifically some UMAPs in clustering QC lesson

update links in "Resources"

1

Check "Resources" section on scRNA-seq schedule page. Some broken links. Also, link the new DBMI materials for using R and RStudio on O2

more challenging exercises

1

We should add exercises which require more thinking and applying rather than just running code (feedback from surveys)