-
Hi,
I am interested in testing the PARC in more datasets. I am wondering what is the source of the true labels? do you use the labels provided by the original papers? For example, the labels in the …
-
### Name of the tool
CellRanger ARC
### Tool homepage
https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc
### Tool description
Add comp…
-
Would it be possible to add an option to run VDJ analysis using the IMGT database as the reference (as opposed to vdj_GRCh38_alts_ensembl-5.0.0, the current reference)? 10X provides a build script fo…
-
Many thanks to @edg1983 and @ewels for the cellranger module https://github.com/ewels/MultiQC/pull/1821. Cellranger count is most commonly ran with GEX data only, but can also support feature barcode …
-
Hi velocyto team,
I have a quick question regarding the pre-velocyto process using cell ranger. The new Cell Ranger 5.0 has a new "**include-introns**" option for counting intronic reads.
https://…
-
Hi @pmarks!
It seems this repo has no releases from the last year, while there are still several inflight commits as well as pending issues/PRs. I'm willing to help in maintaining and releasing thi…
-
Hello,
I am trying to subset my bam file for each barcode. I have around 20k cells and each of their barcode is in a directory. I have been using the code below to execute subset-bam. It takes arou…
-
- [ ] have a cell_ranger root with subtypes
- [ ] move the make config file modulate be generic/shared for arc and multi
- [ ] count
- [ ] multi
- [ ] mkref
- [ ] mkgtf
- [ ] mkvdjref
- [ ] mkc…
-
Hello,
I am using 10X datasets with Cellranger and I want to use Sierra for AS analysis. I am using Ensembl GRCh38 genome and GTF files and I build my own reference. I used the tutorial from 10X Web…
-
istar is a really nice work!
But I have the following concerning about applying istar to 10× Visium data.
① Usually, the output of 10× Visium data include a folder named spatial, which containing…