学术咖

Month: August 2019

  • Cellranger使用教程

    建库，人和小鼠的数据库可以直接下载，对于无法直接下载的需要自行下载全基因组序列和gtf文件，根据 cellranger mkref构建参考数据库 wget ftp://ftp.ensembl.org/pub/release-97/fasta/danio_rerio/dna/Danio_rerio.GRCz11.dna.primary_assembly.fa.gz gunzip Danio_rerio.GRCz11.dna.primary_assembly.fa.gz wget ftp://ftp.ensembl.org/pub/release-97/gtf/danio_rerio/Danio_rerio.GRCz11.97.gtf.gz gunzip Danio_rerio.GRCz11.97.gtf.gz cellranger mkgtf Danio_rerio.GRCz11.97.gtf Danio_rerio.GRCz11.97.filtered.gtf –attribute=gene_biotype:protein_coding \ –attribute=gene_biotype:lincRNA \ –attribute=gene_biotype:antisense \ –attribute=gene_biotype:IG_LV_gene \ –attribute=gene_biotype:IG_V_gene \ –attribute=gene_biotype:IG_V_pseudogene \ –attribute=gene_biotype:IG_D_gene \ –attribute=gene_biotype:IG_J_gene \ –attribute=gene_biotype:IG_J_pseudogene \ –attribute=gene_biotype:IG_C_gene \ –attribute=gene_biotype:IG_C_pseudogene \ –attribute=gene_biotype:TR_V_gene \ –attribute=gene_biotype:TR_V_pseudogene \ –attribute=gene_biotype:TR_D_gene \ –attribute=gene_biotype:TR_J_gene \ –attribute=gene_biotype:TR_J_pseudogene \ –attribute=gene_biotype:TR_C_gene cellranger mkref –nthreads=80 –genome=ref_zebr_GRCz11 –fasta=Danio_rerio.GRCz11.dna.primary_assembly.fa –genes=Danio_rerio.GRCz11.97.filtered.gtf –ref-version=3.1.0…

  • Seurat使用流程

    seurat软件安装 Depends R (>= 3.4.0), methods if (!requireNamespace(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) BiocManager::install(“Seurat”) CentOS系统安装时要注意gcc的版本 setwd(“D:/Experiment_data/zxj/outs”) library(Seurat) pbl.data <- Read10X(data.dir = “D:/Experiment_data/zxj/outs/filtered_feature_bc_matrix”) dim(pbl.data) #查看行和列 #创建 Seurat 对象与数据过滤。保留在>=3 个细胞中表达的基因；保留能检测到>=200 个基因的细胞。 pbl <- CreateSeuratObject(counts = pbl.data, project = “pbl1907”, min.cells = 3, min.features = 200) #mt-开头的为线粒体基因，这里将其进行标记并统计其分布频率 pbl[[“percent.mt”]] <- PercentageFeatureSet(pbl, pattern = “^mt-“) # 对 pbmc 对象做小提琴图，分别为基因数，细胞数和线粒体占比 VlnPlot(object =…

  • CentOS 6.9 安装R-3.6.1

    根据configure报错下载bzip2、curl、PCRE、xz-lzma、zlib对应的版本 如果是64位的系统，安装bzip2时修改Makefile文件，如下： CC=gcc -fPIC AR=ar RANLIB=ranlib LDFLAGS= BIGFILES=-D_FILE_OFFSET_BITS=64 CFLAGS=-fPIC -Wall -Winline -O2 -g $(BIGFILES) 安装好上边的模块后设置环境变量 export PATH=/home/wuchangsong/packages/bin:$PATH export LD_LIBRARY_PATH=/home/wuchangsong/packages/lib:$LD_LIBRARY_PATH export CFLAGS=”-I/home/wuchangsong/packages/include” export LDFLAGS=”-L/home/wuchangsong/packages/lib” 根据报错做如下操作 sudo yum install texinfo sudo yum install texlive unzip inconsolata.zip cp -Rfp inconsolata/* /usr/share/texmf/ sudo mktexlsr ./configure –prefix=/opt/sysoft/R-3.6.1 –enable-R-shlib –with-readline=yes –with-libpng=yes –with-x=no make -j 80 make install