-
Hi
I have a question: I am running ATACseq analysis and I wanted to know - `Do reads need to be DeDuped before FRiP calculation`
- when I say DeDuped - I mean running MarkDuplicates with `REMOVE_…
-
https://mp.weixin.qq.com/s/FqjykN6BIV6sGTdN43axbQ
ixxmu updated
7 months ago
-
Hi,
I read your paper and did not find the text about initialized node features in the guidance graph (maybe I missed the relevant text..).
In my understanding, each node in that graph is a gen…
-
### Description of feature
Hi nf-core cutandrun team
I would like to ask you a question about the +4 and -5 shifts. It is important to shift the raw reads in the pre-processing step to account for t…
-
I tried to create a coverage plot along with gene annotation, but it seems that I have to choose between having a coverage plot without gene annotation and not having at all.
I found why it is bu…
-
Hello,
I was wondering if you can realign the scATAC-seq data using the newest version of cellranger atac since the deduplication has changed the output fragments significantly (better)?
Best,
…
-
I'm currently working on applying PASTA, and I'm having trouble creating a fragments TSV file using Sinto. I've looked through the documentation and searched online, but I'm still not clear on how to …
-
Hi @satijalab!
Thanks for developing this great tool, which makes it very easy to annotate new single-cell datasets.
I'm the first author of the paper [An Atlas of Cells in the Human Tonsil](htt…
-
Good day!
First of all congrats on the paper! looking forward to try it on our dataset.
We have a dataset where we have integrated paired (truly multiome data) and unpaired (scRNA and scATAC in…
-
Hey,
I am using https://stuartlab.org/signac/articles/pbmc_multiomic on a multiome dataset.
I have 5 samples with 5 different fragment files stored in a folder called "Signac_fragpath" ,
Here is…