-
Hi, I have been using `scry::devianceResiduals()` for preprocessing and transformation in 10x Genomics Visium data, and have been running into some possible stability issues and warnings.
I am runn…
-
Hi,
I did not find the answer to this question. And I am not sure if this is something reasonable to do.
Can I use single cell data generated by SmartSeq as a normal reference to infer CNVs on 10x g…
-
The 10x Genomics Chromium linked reads have a barcode in the first 16 nucleotides of the first read, followed by 7 nucleotides that are no good, followed by 128 nucleotides of template. The second rea…
-
Hi ,thanks for developing such a good tool
and if convenient ,I am looking forward to the part for 10x genomics Chromium 3' library,and very curious about when it will be uploaded.
Thanks!
-
https://github.com/alexdobin/STAR/blob/master/RELEASEnotes.md
-
Hi,
I find threads doesn't work under the following case and I must set -j > 30 to run this command:
![image](https://github.com/snakemake/snakemake/assets/29703450/dea04ba4-a5c9-4301-a573-8a1b74278…
-
This is from Marty on our 10X protocol:
> Experimental procedures followed established techniques using the Chromium Single Cell 5’ Library & Gel Bead Kit (10x Genomics; https://assets.ctfassets.ne…
-
Hi,
Thank a lot for this tools.
I have some 10x genomics scRNA-seq 3'data. So I have one bam file per sample , with barcoded reads represented each cell. I was wondering if I can use this tools…
-
This is something we are looking at over at the https://github.com/Clinical-Genomics/chanjo2 repo.
The current approach is to read the output from the d4 file using `d4tools show`. It would be much…
-
Running TRUST4 on 3' 10X genomics RNA-seq results in B cell inference where no B cells are present, any advice on fixing this issue?