-
Hello,
Section 1.3 of the README reads:
> At this point, we get
> - a scRNA-seq count matrix from cellranger (1.1) with automated filtered cells based on cellranger cutoffs for detecting empty …
-
When I use "CITE-seq-Count-R1./ SRR13724311_S1_L001_R1_001.fastq.gz-R2 SRR13724311_S1_L001_R2_001.fastq.gz-t Cmca9_tag_list_utf8.cfa-cbf 1-cbl 16-umif 17-umil 28 -cells 10000-o OUTFOLDER "is always no…
-
Hello,
I'm using STARsolo for demultiplexing datasets from multiplexed bulk RNA-seq protocols (here in particular the BRB-seq protocol).
In general, it works like a charm, and it's super fast! S…
-
Dear author:
I used droplet based method to generate the data, and followed the vignette. However, calculateEdgeStats returns a tibble with 'NA' values. What might be the problem? Thanks.
![image](h…
-
Hi Will,
quasi-UMIs seem like a great way to feed non-UMI data to UMI-based methods. Thank you for all your work and this R package.
When trying it out with some subset of the Tabula Muris bone ma…
-
I have a quick question about the snRNA-seq data of CCRCC samples that were used in this study. I downloaded the data from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE240822, following the d…
-
Hi,
Thank you for developing such a wonderful tool!
I am currently looking to utilize the existing CNV profile via the `segs_consensus_fix `parameter to establish definitive CNV boundaries and stat…
-
For several datasets I have pulled from the literature, the median UMIs per barcode predicted by `bustools inspect` is much higher than the actual median UMIs per barcode in the output of `bustools co…
-
### Ask away!
The pipeline has run successfully using `--kit 'visium:v1'` with `2.2.0` The output generated are as follows
```
config_stats.json
gene.expression.mito-per-cell.tsv
gene.expressi…
-
Hello,
I'm getting the following error during UMI correction, when running CITE-seq-Count 1.4.5, Python 3.8.
```
Correcting umis
Traceback (most recent call last):
File "/data/home/hmy961/c…