Jeremy Simon

Error with dropEst->velocyto workflow

6

I've been trying to follow your [vignette](http://velocyto.org/velocyto.py/tutorial/cli.html#run-dropest-run-on-dropseq-indrops-and-other-techniques) for analyzing Drop-seq data with dropEst, then running velocyto. However I've encountered an error during `dropest_bc_correct` that I can't seem to navigate around....

Issue with droptag/dropest on SPLiT-seq data, no CBs recognized

1

I'm trying to use dropEst to process SPLiT-seq data, specifically using SRR6750042 from GSE110823 as a test run. Note that I am able to successfully run dropEst on the example...

Add support for stranded libraries?

8

I'm wondering how possible it would be to create gene x cell matrices separated by strand in the case of stranded libraries. In other words, dropEst currently summarizes coverage over...

What types of mismatches are supported in `seqkit locate`?

4

Hi, could you please clarify what sorts of mismatches are supported in `seqkit locate`? Is it single base changes only or are insertions and/or deletions allowed as well? `fish` seems...

Clarification on how matches are determined within trackClonotypes?

2

## 📚 Documentation Hi, I'm reading in 10x scTCR data processed via `cellranger` and using `trackClonotypes` to tabulate and plot proportions across samples. Is there documentation somewhere about how a...

Possible to add support for 10x VDJ?

2

The answer here could simply be 'no' 😄 but as this question came up recently for me, and it is one I've seen mentioned on the `nf-core/scrna` slack, I figured...

Error at SIMPLEAF_INDEX for user supplied genome/annotation

1

### Description of the bug I'm having some trouble getting the `test` data to run via `singularity` with `alevin`, specifically if I supply my own genome/annotation. It's failing at `SIMPLEAF_INDEX`...

Hey Team Pufferfish- I'm just wondering your opinions on best practices if I were to want to index many (hundreds? thousands?) of whole human genomes and then query them. Let's...

Update documentation to include recommended processing for 10x scRNA 5' V2

3

Hey @rob-p and @Gaura - I've started working with 10x 5' V2 data, and wanted to utilize `alevin-fry` for processing of the raw data. I initially found some discussions from...

Is it appropriate/possible to run IntegrateData following GLM-PCA?

1

Hi @willtownes, My typical Seurat workflow for multiple samples and conditions is to run PCA followed by CCA-based integration (now `IntegrateLayers` in Seurat v5), then identify one joint set of...