Tag: GEX

I have a CITE seq experiment where the GEX and antibody capture were mapped separately, so that I have to load in two different matrices. adata_adt = sc.read_10x_mtx( “data/CITESeq_381/”, gex_only = False ) adata_gex = sc.read_10x_mtx( “data/GEX_381/filtered_feature_bc_matrix/”, gex_only = True ) I subset to only cells with GEX and ADT…

cellranger count: an extremely low rate of correct barcodes was observed 1 I am new to cellranger. And I tried to run cellranger count for a fastq.gz file. My code is something like this: (** is just to replace my address name due to privacy issue) fastq-dump –outdir fastq –split-files…

I’m using CellRanger to analyze some RNA-seq data I have but I’m having a bit of trouble knowing if I’m doing the preprocessing steps correctly. This is the folder of Fastqs that I have: Control_GEX_S1_L003_I1_001.fastq.gz Treatment_BCR_S6_L004_R2_001.fastq.gz Control_GEX_S1_L003_I2_001.fastq.gz Treatment_GEX_S2_L003_I1_001.fastq.gz Control_GEX_S1_L003_R1_001.fastq.gz Treatment_GEX_S2_L003_I2_001.fastq.gz Control_GEX_S1_L003_R2_001.fastq.gz Treatment_GEX_S2_L003_R1_001.fastq.gz Control_GEX_S1_L004_I1_001.fastq.gz Treatment_GEX_S2_L003_R2_001.fastq.gz Control_GEX_S1_L004_I2_001.fastq.gz Treatment_GEX_S2_L004_I1_001.fastq.gz Control_GEX_S1_L004_R1_001.fastq.gz Treatment_GEX_S2_L004_I2_001.fastq.gz Control_GEX_S1_L004_R2_001.fastq.gz Treatment_GEX_S2_L004_R1_001.fastq.gz…

Low percentage of ‘Fraction Antibody Reads Usable’ in Feature Barcode Cell Ranger output 0 Hi, I have a question regarding the Cell Ranger output of scRNAseq with Feature Barcode. I’ve performed the standard Cell Ranger count using cellranger-6.0.0 and the following arguments: –id=A_GEX –libraries=library_A.csv –transcriptome=/……/refdata-gex-GRCh38-2020-A –feature-ref=/…../10x_feature_ref.csv When looking at the…

Merging FASTQ files with Cellranger 1 I’m new to CellRanger and am doing genome alignments on a set of .fastq files which I did not generate myself. The files have are in a folder structure where there are 10 folders in total, each of the five samples L1-L5 (or SIGAA-SIGAE)…

Human samples Placental and decidual samples used for the in vivo and in vitro profiling were obtained from elective terminations from: The MRC and Wellcome-funded Human Developmental Biology Resource (HDBR, www.hdbr.org), with appropriate maternal written consent and approval from the Fulham Research Ethics Committee (REC reference 18/LO/0822) and Newcastle and…

Cellranger count with error information “… which wasn’t expected, or isn’t valid in this context” 1 Hello everyone, I just practiced the scRNAseq upstream analysis from cellranger official tutorial. But I met a small problem but it stopped me from going the next step. I followed the tutorial exactly but…

STARsolo issue 0 hello, I’m performing STARsolo on pbmc fastq files and I’m using the reference genome from 10*genomics but I have this issu that I can’t understand (the reference genome is indexed) STAR version: 2.7.10b compiled: 2022-11-01T09:53:26-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Mar 13 14:42:48 ….. started STAR run Mar 13 14:42:48 ……..

I don’t think you can reduce the number of reads required for autodetection, and it would be a bad idea anyway, because the guess could go wrong. From 10X Q&A: TotalSeq B is specifically designed to be compatible with the Single Cell 3’ v3 and 3.1 workflows And from CellRanger…

Cell lines Immortalised HA1E (hTERT and SV40ER) and tumourigenic HA1ER cells (hTERT, SV40ER and HRAS-G12V) from stepwise tumourigenesis models generated from normal human embryonic kidney cells were obtained from Dr. Hahn (Broad Institute of MIT and Harvard, Cambridge, USA). Cells were cultured in DMEM (1 g/L glucose) (Gibco, cat. #10567014) supplemented…

Signac/DeepTools data exchange 0 Hi all, I’m trying to analyze some DOGMA single cell data (GEX+ ATAC). I have been following the tutorials from Seurat + Signac packages to analyze the ATAC part of the data (this one and this one), and so far everything is working fine.My problem is…

Sc-RNA seq 5’ V2 PE auto detected by CellRanger as R2 only chemistry 0 I submitted in house lab-made libraries to a core to run our scRNA-seq. The libraries were made using a 5’ V2 PE kit. Dual index. So we got I1, I2, R1 and R2 GEX FASTQs back…

I have some marmoset snRNA reads that I want to align with the reference transcriptome using cellranger. The primary assembly for marmoset is available here, which is broken down into 22 parts. However, cellranger mkref only accepts one .fa file to generate the transcriptome. I tried concatentaing all the extracted…

R: Summarize an eqtl Object summary.eqtl {GenomicTools} R Documentation Summarize an eqtl Object Description Summarizes and prints an eqtl object in an informative way. Usage ## S3 method for class ‘eqtl’ summary(object, sig=0.01, …) Arguments object Object of class eqtl. sig Significance level to print. … Additional parameters. Details This…

Name Last modified Size Description Parent Directory   –   org.pathvisio.core.jar 2012-03-08 16:50 1.4M   org.pathvisio.core/ 2012-03-08 16:50 –   org.pathvisio.deskto..> 2012-03-08 16:50 238K   org.pathvisio.desktop/ 2012-03-08 16:50 –   org.pathvisio.gex/ 2012-03-08 16:50 –   org.pathvisio.gexplu..> 2012-03-08 16:50 53K   org.pathvisio.gui.jar 2012-03-08 16:50 208K   org.pathvisio.gui/ 2012-03-08 16:50 –  …

cellranger count DETECT_COUNT_CHEMISTRY (failed) 0 I am learning scRNA-seq and the tutorial I follow uses dataset (1k pbmcs from healthy donor) from 10X genomics website. I downloaded fastq and reference transcriptome files and ran following command. cellranger-6.1.1/cellranger count –id pbmc_1k_v2_example –transcriptome /home/murat/Share/single_cell/refdata-gex-GRCh38-2020-A –fastqs /home/murat/Share/single_cell/pbmc_1k_v2_fastqs I get following message. Martian Runtime…

cellranger count help 0 these were original data from sequencing company and then i compressed these files into two files R1 and R2 /data01/chenyu/sc/cellranger-6.1.1/cellranger count –id=cellranger_szdxb015 –fastqs=/data01/chenyu/sc/sortData/191527A_SZdxb01_5 –sample=SZdxb015 –transcriptome=/data01/chenyu/sc/refdata-gex-GRCh38-2020-A –localcores=20 –nosecondary error occured： FASTQ header mismatch detected at line 4 of input files “/data01/chenyu/sc/sortData/191527A_SZdxb01_5/SZdxb015_S1_L001_R1_001.fastq.gz” and “/data01/chenyu/sc/sortData/191527A_SZdxb01_5/SZdxb015_S1_L001_R2_001.fastq.gz”: file: “/data01/chenyu/sc/sortData/191527A_SZdxb01_5/SZdxb015_S1_L001_R1_001.fastq.gz”, line: 4…

  I’ve been trying to setup an analysis pipline for RNAvelocity in AWS EC2. I used one of the 10x dataset, 10k Peripheral blood mononuclear cells (PBMCs) from a healthy donor, Single Indexed, as a test model to setup the pipeline. For speed and cost saving, I first used samtools…

Corelate TCR data to clusters/GEX/CITEseq data 1 Hello everyone, I just added my TCR VDJ data as metadata to my Seurat object (as described in the tutorial here). So, I basically ended up with two different collumns of metadata where my barcodes are assigned to the clonotypes and the cdr3…