Tag: GEX

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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