MGI DNBelab C Series High-throughput Single-cell RNA Library Preparation Set V3.0, Seurat

Dear All,

I would like to know if I can input MGI single cell rna-seq data into Seurat for analysis?

I only used 10X data for seurat before.

What will be the "filtered_feature_bc_matrix" which includes barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz in MGI dnbc4tools output?

thanks!

rna-seq seurat single-cell mgi

• 1,431 views • link

updated 2.2 years ago by bk11 •

• written 2.2 years ago by yau •

1 answer

Did you check this link below where it show how Seurat or Scanpy can be used for downstream analyses from MGI dnbc4tools output?

https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software/blob/version2.0/doc/io.md

• 0 views • link

written 2.2 years ago by bk11 •

More posts like this

Read spatial data from GSM8557976 using Seurat
written 10 months ago by tujuchuanli

Hi, I am trying to load the spatial data from GSM8557976 using Seurat. The dataset includes seven files: "barcodes.tsv.gz", "features.tsv.gz", "matrix.mtx.gz", "scalefactors_json.json.gz", "tissue_hires_image.png.gz", "tissue_lowres_image.png.gz", and …
Single cell multiomics data i.e, sc(RNA+ATAC) seq data tar file
written 12 months ago by Rupanjali •

Hello everyone, I have downloaded the dataset GSEXXXXXX from NCBI which provides single-cell multiome data (scRNA-seq + scATAC-seq). For each sample, the .tar.gz archive (GSEXXXXXX_10x_filtered_matrix.tar.gz) …
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
written 2.2 years ago by yau •

Dear all, I am recently running FindMarker and EnhancedVolcano in Seurat for single-cell RNA-seq data. However, the value of -log10p value of most of the …
convert matrix files from 10X (single cell) to h5 file
written 2.8 years ago by Sara

For my single cell data, I have matrix files from 10X including (`barcodes.tsv.gz`, `features.tsv.gz`, `matrix.mtx.gz`) for all my samples. I am trying to convert them …
SEURAT : loading via h5 file and applying min.cells and min.features
written 3.9 years ago by ZheFrench

Usually from publicly available 10X spatial/scRnaseq, you end up with 4 files barcodes/counts/features/tissuesMap(for spatial only). In my workflow, I generally use `CreateSeuratObject` and apply `min.cells …
How to convert 10x matrix.mtx.gz files to hdf5 format?
written 4.1 years ago by johnny rocketfingers •

I have a bunch of folders containing barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz from the Cellranger Count output for a single-cell dataset that was sent to me …
Merge Gene expression and Antibody capture data in Seurat
written 5.2 years ago by chi.delta •

Hey everyone, I am currently analyzing some mouse 10x scRNA seq data ( after the mapping with cellranger I got 3 output files: matrix.mtx.gz, features.tsv.gz, …
GEO datasets-Single cell RNAseq analysis using seurat
written 5.4 years ago by LionisOne •

I'm trying to look through a published dataset to check for gene expression for my own project. I am having trouble finding materials to teach …
Count Matrix from Single cell RNA
written 6.4 years ago by David_emir

Hi All, We did Single Cell RNA data analysis from 25 diseased patients. The Vendor sent 25.MTX files to us. The files we received is …
RaceID3 using 10x datasets
written 6.6 years ago by Seigfried

Hello I wish to cluster my single cell 10x data using RaceID3. However, I cannot load my 10x data into RaceID using their function SCseq …