Tools to remove ambient RNA from single-nuclei data
Dear all,
can anybody recommend a good tool to remove ambient RNA from single-nuclei data?
Thanks, Chris
single-nuclei rna-seq
ambient rna
• 1,335 views
•
link
written
by
christianhinze •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Ambient RNA correction when most of the ambient comes from a specific cell type of interest
written by txema.heredia •Hi, I am analyzing single nuclei RNA-seq of patient biopsies. The samples are tumor metastases in the liver. 3 patients, 2 samples form each. I …
-
What percentage of intronic reads should I expect in single-cell vs single-nuclei?
written by txema.heredia •Hi, I'm, analyzing a single-nuclei dataset with not-so good quality, and I am trying to understand what went wrong. These are cancer samples. Biopsies of …
-
Should use Ambient RNA detection software for filtered_bc_matrices from Cell Ranger for snRNAseq
written by biotrekker •Sorry still new to this. I have ~100 samples with 7k cells at least from the human brain (diseased and not-diseased). So far I have …
-
Using soupX on single nucleus RNA seq data
written by happymuffin24 •Dear Community! This is my first post here and I *thank you in advance* for your input. I have a 1**0x single nucleus dataset** of …
-
ambient RNA removal tool preferences?
written by benjamin.pyenson •Hi, I have run souporcell successfully on single-nucleus RNAseq filtered barcode (bc) matrix generated from CellRanger (v.6.1.2), which generates an experiment-wide ambient RNA % of …
-
Inter-sample variance explained
written by christianhinze •Dear all, I am working with single-cell gene expression data of N samples on roughly 800 different features (genes). The cells of each sample come …
-
to consider only intronic reads in cell ranger pipeline
written by DataminerHello community, I am processing some single nuclei RNA seq data and unfortunately while performing the experiment there was high leakage of mRNA and that …
-
Tumor Purity and miRNA / small RNA pipeline
written by ResearchRDear all, I would like to ask you for two suggestions: 1. If got an incredible amount of miRNA-Seq data. Can anybody of you recommend …
-
Fusion gene partner
written by KorsociusDear all, I have question. I've got a DNA data from semiconductor parallel sequencing (single end). How can get fusion gene result from this? Could …
-
Samtools MPILEUP on single-end/paired-end data
written by christianhinze •<p>Hi everybody,</p> <p>for variant calling, i am using samtools mpileup.</p> <p>as far as i know, mpileup is by default ignoring certain reads (duplicate, failed QC, …
Can you clarify what do you mean by
ambient RNA?