• Sequencing with 10X genomics

    I am planning to do single cell RNA-seq with 10X genomic platform. I was wondering if there are ...

  • Best way to perform single-cell RNA-seq normalization

    Is there an optimal way to do single-cell RNA-seq counts normalization? Most RNA-seq normalizatio...

  • bcl2fastq2: how to correctly use the --use-bases-mask for different sequencing methods by Illumina ?

    Hello,

    I need your help to address the parameter found in [bcl2fastq2][1] tool when demultiplexi...

  • How to find percentage of a gene (eg.Ppbp) for condition A and condition B from 10X Single Cell RNAseq?

    Hi All,

    I am working on a single cell rnaseq dataset for two conditions. 10X genomics protocol a...

  • how to judge the 10X genomics single cell data quality

    Dear all,

    i am analysis 10X genomics single cell data these days, but i donot know the specific ...

  • Calculating differential expression genes between two sample sequenced using 10x

    I have treatment and control samples single cell sequencing performed using 10x method. I wanted ...

  • How to Merge 2 Technical Replicates From the same cDNA library (but run on different sequencers)?

    Could anyone inform me about the best approach for merging 2 technical replicates **from the same...

  • Extracting high quality reads from partially failed 10X single cell RNA-, ATAC-seq sequencing run

    I seek advice as to the best strategy to salvage high quality reads from a 10X single cell RNA-, ...

  • single cell analysis: normalize gene expression across samples

    Hi,

    I have results from a 10x genomics single cell experiment.
    In the experiment I have sequence...

  • Converting scRNA-Seq to Bulk-RNASeq

    for the initial analysis of our data set we would like to convert our single-cell RNA-Seq into Bu...

  • Should I aggregate expression matrices from cell hashed and non-hashed libraries with cellranger?

    Dear all,

    We performed a scRNA-seq experiment using the [cell hashing](https://genomebiology.bio...

  • Low mappable reads using NugenOvation Single Cell RNA-Seq System

    I created single-cell RNAseq libraries from neurons and sequenced them at depths of ~10 million r...

  • the analysis of multiple samples of 10X scRNA-seq

    Dear all, greetings

    i'd like to ask you for a piece of advise please : we have 3 scRNA-seq samp...

  • Single cell Expression Analysis

    Hi All,

    I have 6,000 single-cell expression counts from 49 head and neck squamous cell carcinom...

  • Depth of Single Cell RNA seq experiment

    Hello,

    I am new to this field, and would greatly appreciate an answer to this question.

    I am l...

  • Expression plots of some genes of interest from scRNA data for each library

    I am new to scRNA analysis and confused on a simple problem.

    I have some genes of interest and I...

  • Single cell RNA-seq analysis

    Hi guys
    I am new to biological field and single cell RNA seq analysis , and I do not have idea h...

  • Clustering resolution single-cell RNA-seq

    Hi,

    I have a question about how to decide on the clustering resolution to use for single-cell RN...

  • Bulk RNA seq vs Sinlge Cell RNA seq correlation comparison

    I want to compute the correlation between bulk-RNA-seq data(Nugen Ovation RNAseq V2 amplified lib...

  • Downsampling reads vs. Seurat normalisation

    Hi,

    I am performing combined analysis of three 10x Genomics scRNA-seq samples using Cell Ranger ...

  • What does a 'normal' FASTQC report look like for scRNA-seq data?

    I'm interested specifically in 'failures' I got on R2 (R1 being just the barcode + UMI). Note thi...

  • Average insert size and standard deviation among R1 and R2 scRNA-seq 10X

    Hi guys,
    I need to upload in a public repository single cell paired ends data from 10X, i.e. I h...



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