Tag: GEX

Cell ranger multi for demultiplexing FB files and GEX files

Cell ranger multi for demultiplexing FB files and GEX files 0 I have my feature csv file which is multiplexing capture, i have feature barcode fastq files, gex fastq files and i was trying to run cell-ranger multi but this error shows up (error] Deplex Error: No valid tags were…

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CYP1A2 expression rather than genotype is associated with olanzapine concentration in psychiatric patients

Owen, M. J., Sawa, A. & Mortensen, P. B. Schizophrenia. Lancet 388, 86–97 (2016). Article  PubMed  PubMed Central  Google Scholar  Bhana, N., Foster, R. H., Olney, R. & Plosker, G. L. Olanzapine: An updated review of its use in the management of schizophrenia. Drugs 61, 111–161 (2001). Article  CAS  PubMed …

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Index of /~psgendb/birchhomedir/public_html/doc/local/pkg/PathVisio/modules/org.pathvisio.gex/build/org/pathvisio/gexplugin

Name Last modified Size Description Parent Directory   –   Activator.class 2012-03-08 16:50 1.0K   ColumnTableModel$1.c..> 2012-03-08 16:50 1.0K   ColumnTableModel$Hig..> 2012-03-08 16:50 2.4K   ColumnTableModel.class 2012-03-08 16:50 1.7K   GexImportWizard$1.class 2012-03-08 16:50 244   GexImportWizard$Colu..> 2012-03-08 16:50 1.4K   GexImportWizard$Colu..> 2012-03-08 16:50 1.6K   GexImportWizard$Colu..> 2012-03-08 16:50 1.4K  …

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SeqMatic Adds Visium Spatial Gene Expression to its 10x Genomics Certified Service Provider Portfolio

Fremont, California – October 2nd, 2023 – SeqMatic, a leading provider of next-generation sequencing (NGS) and omics services, is proud to announce that it has received Visium Spatial Gene Expression and Visium Spatial Gene Expression for FFPE Certifications from 10x Genomics. These certifications further demonstrate SeqMatic’s commitment to delivering efficient…

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How to get the gft file to run velocyto for velocity analysis?

How to get the gft file to run velocyto for velocity analysis? 1 You need the same GTF file that was used during mapping of your 10x data. If you used CellRanger and it was mouse (given you used recent CellRanger) you can find it in the CellRanger folder under…

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Single-cell brain organoid screening identifies developmental defects in autism

Stem cell and cerebral organoid culture conditions Feeder-free hES cells or iPS cells were cultured on hES cell-qualified Matrigel (Corning, catalogue no. 354277)-coated plates with Essential8 stem cell medium supplemented with bovine serum albumin (BSA). H9 embryonic stem cells were obtained from WiCell. Cells were maintained in a 5% CO2 incubator at 37 °C….

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Single-cell massively-parallel multiplexed microbial sequencing (M3-seq) identifies rare bacterial populations and profiles phage infection

Bacterial strains and growth conditions for eBW1 B. subtilis 168 and E. coli (MG1655) were streaked out from a frozen glycerol stock onto an LB plate and grown overnight at 37 °C. Following a night of growth, a single colony was picked and inoculated into 5 ml of LB broth and grown…

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Dynamic thresholding and tissue dissociation optimization for CITE-seq identifies differential surface protein abundance in metastatic melanoma

Workflow overview CITE-seq and cell hashing were performed on liquid and solid tissue biopsies (Fig. 1a, b). Experimentally, cells from 17 samples (Supplementary Data 2) were hashed and stained with a panel of 97 antibodies (Supplementary Data 2) covering key as well as exploratory immuno-oncology markers resulting in 57,261 cells after preprocessing and…

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Seurat IntegrateData function returning an error

Hello, I am trying to integrate the data by correcting for batch effects per patient and I’m running into this error while executing the IntegrateData function, how do I fix this? Is it because the sepsis2HTO_HAB3 (7th dataset) has too few samples (66) to be properly integrated? analyseFinalList = function(objlist,…

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Input FASTQ file ended prematurely

Cellranger count error: Input FASTQ file ended prematurely 0 Hi all, I am trying to align and produce counts form some scRNA-seq using CellRanger 7.1.0. The fastq files for input are of the following format (for illustration): SI-GA-A1_1_S1_L001_I1_001.fastq.gz SI-GA-A1_1_S1_L001_R1_001.fastq.gz SI-GA-A1_1_S1_L001_R2_001.fastq.gz SI-GA-A1_2_S2_L001_I1_001.fastq.gz SI-GA-A1_2_S2_L001_R1_001.fastq.gz SI-GA-A1_2_S2_L001_R2_001.fastq.gz SI-GA-A1_3_S3_L001_I1_001.fastq.gz SI-GA-A1_3_S3_L001_R1_001.fastq.gz SI-GA-A1_3_S3_L001_R2_001.fastq.gz SI-GA-A1_4_S4_L001_I1_001.fastq.gz SI-GA-A1_4_S4_L001_R1_001.fastq.gz SI-GA-A1_4_S4_L001_R2_001.fastq.gz and…

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A universal tool for predicting differentially active features in single-cell and spatial genomics data

singleCellHaystack methodology For a detailed description of the original singleCellHaystack implementation (version 0.3.2) we refer to Vandenbon and Diez19. In brief, singleCellHaystack uses the distribution of cells inside an input space to predict DAFs. First, it infers a reference distribution \(Q\) of all cells in the space by estimating the…

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How to add VDJ clonotyping data to Seurat object of scRNA-seq

How to add VDJ clonotyping data to Seurat object of scRNA-seq 0 I have performed CITE-seq (ADT, GEX, TCR) in 20 PBMC samples, consisting of responders and non-responders. By following Seurat tutorial, I performed standard pre-processing process, merging seurat object, integration, and drew the UMAP and compared the freq. of…

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cellranger count matrix

Hello everyone, I am trying to run the cell ranger count using the following command. cellranger-7.1.0/cellranger count \ –id project1 \ –transcriptome refdata-gex-mm10-2020-A \ –fastqs NK_dataset/ \ –sample 1013MJ1,1013MJ2,1013Saline1,1013Saline2,106MJ1,106MJ2,106Saline1,106Saline2,113MJ-1,113MJ-2,113Saline1,113Saline2 \ –expect-cells 85000 \ –localcores 8 \ –localmem 100 I am using doing this on the cluster and due to some…

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demultiplex bcl files from 10X genomics and generate fastq file for each sample separately

demultiplex bcl files from 10X genomics and generate fastq file for each sample separately 0 I have bcl files from 10X genomics and trying to demultiplex them and generate fastq files. to do so, I m using cellranger mkfastq and once I have fastq files I will use cellranger multi….

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Help concatenating var for cite seq – scanpy

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…

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an extremely low rate of correct barcodes was observed

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…

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Need to specify “–chemistry” argument in “cellranger count”

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…

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Low percentage of ‘Fraction Antibody Reads Usable’ in Feature Barcode Cell Ranger output

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…

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Merging FASTQ files with Cellranger

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)…

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Spatial multiomics map of trophoblast development in early pregnancy

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…

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Cellranger count with error information “… which wasn’t expected, or isn’t valid in this context”

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…

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STARsolo issue

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 ……..

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scrnaseq – In cellranger, can I change the minimum number of reads for autodetecting chemistry?

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…

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BdLT-Seq as a barcode decay-based method to unravel lineage-linked transcriptome plasticity

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…

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Signac/DeepTools data exchange

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…

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Sc-RNA seq 5’ V2 PE auto detected by CellRanger as R2 only chemistry

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…

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transcriptome – How to combine multiple .fasta files of primary assembly from Ensembl into one for sequence alignment?

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…

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R: Summarize an eqtl Object

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…

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Index of /~psgendb/birchhomedir/doc/local/pkg/PathVisio2.0.11/modules

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 –  …

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cellranger count DETECT_COUNT_CHEMISTRY (failed)

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…

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cellranger count help

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…

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Disappearing CB, the bam tag after samtools sort -t CB

  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…

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Corelate TCR data to clusters/GEX/CITEseq data

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…

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