报错一: mkref has FAILED Error building referencepackageErrorwhileparsing GTF file/storagenew/YZY_new/Single-nucleus-RNA+ATAC/Reference_for_Cellranger_arc/Dmel/dmel-all-r6.37.gtf Supplied GTFisinvalid.This row['X','FlyBase','exon','19961689','19961845','.','+','.','gene_id "FBgn0031...
还需配置mm10_egfp.config文件: {organism:"mouse"genome:["mm10"]input_fasta:["new_ref/genome.fa"]input_gtf:["/new_ref/genome.gtf"]non_nuclear_contigs:["chrM"]input_motifs:"refdata-cellranger-arc-mm10-2020-A-2.0.0/regions/motifs.pfm"} 最后运行构建ref的命令: cellranger-atac mkref -...
构建index文件可以使用cellranger中的工具 --cdllranger mkrek cellranger mkref \ --genome=refern_data \ --nthreads=10 \ --fasta=genes.fa \ --genes=genes.gtf --genome:生成索引的目录 --nthreads:线程数 --fasta:基因组序列 --genes:基因组注释文件(.gtf) 建议使用官网下构建好的索引,没有区别,...
must besetto'ARC-v1'[default:auto]--no-librariesProceedwith processingusinga--feature-refbut noFeatureBarcodelibraries specified with the'libraries'flag--check-library-compatibility<true|false>Whetherto checkforbarcode compatibility between libraries.[default:true][possible values:true,false]--min-crispr...
cellranger mkref:10x 单细胞转录组测序的参考基因组准备。 cellranger vdj:10x VDJ 数据文库分析,scTCR/BCR(T/B细胞受体) 文库数据分析 cellranger reanalyze:输入生成的矩阵,调整不同的参数进行降维、聚类。 注意,不同下机数据对应的处理软件不一样
New Cellrangerarc modules (#3576) * Clean commit for cellranger-arc modules * Clean commit of cellranger-atac * Small wording change to README * changes to test_data.config * Exlcuding cellrangeratac from conda * Bugfix for cellrangeratac mkref * Bugfix for cellrangerarc mkref * Ex...
wget https://cf.10xgenomics.com/supp/cell-atac/refdata-cellranger-arc-mm10-2020-A-2.0.0.tar.gz 系统配置 官网有最低的系统配置要求,基本上得上服务器才行: 不同配置的性能表现及分析时间: 文件拆分 ❝ cellranger-atac工作流程的第...
Reference packages for human (GRCh38) and mouse (mm10) compatible with Cell Ranger ARC are available fordownload. You can alsocreate a reference packageusingcellranger-arc mkrefstarting with a genome assembly FASTA file, a GTF file of gene annotations, and optionally a file of transcription fac...
cellranger mkref --help cellranger mkref --genome=NAME --fasta=PATH --genes=PATH [options] ArgumentDescription --genome Required. Unique genome name(s), used to name output folder [a-zA-Z0-9_-]+. Specify multiple genomes by specifying the --genome argument multiple times; the output ...
Or generatea custom referencewithmkref --feature-refPath to aFeature Reference CSV filedeclaring the Feature Barcode reagents used in the experiment.Required for Feature Barcode analysis. --target-panelPath to aTarget Panel CSV filedeclaring the target panel used, if any.Required for Targeted Gene...