Doctor G

DimProj from RunFastMNN: non-conformable arguments

4

I've been using RunFastMNN to align partially overlapping datasets. It works great in this context, but I run into an issue not in downstream analyses, but in downstream presentations like...

Hello, Is there any guidance you can provide regarding the differences between sctransform::compare_expression, as described in your sctransform tutorial, and Seurat::FindMarkers (whose more general framework includes a LRT and t-test)?...

Error in arrow file creation (.addGeneScoreMat): "HDF5. Dataset. Unable to initialize object"

6

Hi, I have an issue that I suspect may be related to the recently fixed error (https://github.com/GreenleafLab/ArchR/issues/395) in saving tile matrices when there is no coverage (short scaffold). During arrow...

Issue in .getFragsFromArrow (and thus addGroupCoverages) when nFrags = 1

3

I ran into a small issue when running addGroupCoverages on my terrible non-model species genome. [ArchR-addGroupCoverages-765f62f12d5f-Date-2021-04-18_Time-23-35-59.log](https://github.com/GreenleafLab/ArchR/files/6332245/ArchR-addGroupCoverages-765f62f12d5f-Date-2021-04-18_Time-23-35-59.log) > addGroupCoverages(ArchRProj = projSpurp_doubletRemoved_filtered2, groupBy = "Clusters_doubletRemoved_filtered", threads = 1, force = TRUE) #just...

troublet issue possible involving RUST (thread 'main' panicked)

8

I'm using the most recent (e.g. two days ago) singularity container and getting the following error (repeated here from trying to run just the troublet part in isolation) ``` %...

Where on earth are the intermediate files

1

I don't actually know if I have an issue yet, but I am surprised that after 30 min running this command: > alignmentSieve -b /data/gpfs-1/users/amonaco_m/project_work/projects/12_DrosophilaF1Hyb_scSeq/2_10XscATAC/6_totalCounts/Hyb2Dsec/Hyb2Dsec/outs/possorted_bam.bam --minMappingQuality 10 --filterMetrics ~/scratch/bam_storage/dsec.sieve.log.txt -o...

Discussion question -- is it normal to take so long?

3

So I am abusing this tool a bit to look not at CITE-seq barcodes, but at a TRACE-seq barcoding experiment in which my specific experiment has (empirically) about 66,000 barcodes....

This isn't a bug....its a feature request.....can one turn off the reverse complement

1

Sometimes the data are strand invariant (e.g. ChIP) and, thus, so are the attributions we wish to interpret. But sometimes your model is Decima and the whole thing most definitely...