-
CP257 errored as described in broadinstitute/pooled-cell-painting-profiling-recipe#73
```
All sites complete.
Summarizing 4684 sites in batch: 20210422_6W_CP257.
/home/ubuntu/miniconda3/envs/poo…
-
We've seen this error before, it has to do with the machine not being large enough to write out the full single cell file per plate.
Here is the error where halted:
```bash
Building single file…
-
@hillsbury and I chatted about adding a single cell normalization option in two different scenarios:
1. When using a single file (output_one_single_file_only set to true)
2. When using single cell…
-
@ErinWeisbart - I am trying to rerun this step in the recent pooled dataset. It was working smoothly until line 471. I paste the error statement at the end of this issue (file paths intentionally obsc…
-
For our notes, there are two alternate paths that either replicate cytominer-database functionality or obviate its need
1. @gwaygenomics works directly with CSVs in pooled Cell Painting experiments…
-
A major shortcoming of the current approach is forking `profiling-recipe` means that you are limited to one fork (for a given GitHub account). Consider this scenario:
1. I am `user-A` and I create …
-
Currently, the barcodes called, quality of barcodes called, and sgRNA assigned to barcode are all output by CellProfiler with no option to modify in-recipe.
It would be helpful to be able to perform …
-
In a recent dataset, the `image_metadata.tsv` was >300MB which is larger than the allowed file size for github. We should do two things:
- Compress this to a `.tsv.gz` file
- Fix here: https://g…
-
Right now, only one file indicating perturbation abundances is output _per site_. We should make retrieving a per-plate perturbation abundance easier, by summarizing perturbation counts in an addition…
-
A potentially fun analysis would be to evaluate how the different moa/target annotations updated over time (in different CLUE drugs/samples versions) influence moa/target recall.
Essentially, we wo…