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Make sure you are using the complete and correct path to the Cellranger directory and make sure every entry in .bashrc file is valid. ... Hello, Everyone, I tried to use mat2csv convert matrix to csv format. Thanks in advance for any... cellranger mkref failed .

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cellranger单细胞分析流程主要分为:数据拆分 cellranger mkfastq、细胞定量 cellranger count、GEM整合 cellranger aggr、定制调整 cellranger reanalyze。 还有一些用户可能会用到的功能:mat2csv、mkgtf、mkref (构建索引)、vdj、mkvdjref、 testrun (测试软件是否安装成功和输出结果的结构 ...

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cellranger/2.1.1¶ name cellranger version 2.1.1. description An analysis pipeline for processing Chromium single-cell RNA-sequences. Capable of converting BCL files from Illumina sequencing systems to FASTQ file formats.

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----- Usage: cellranger mkfastq cellranger count cellranger aggr cellranger reanalyze cellranger mat2csv cellranger mkgtf cellranger mkref cellranger vdj cellranger mkvdjref cellranger testrun cellranger upload cellranger sitecheck ----- Usage: cellranger mkfastq cellranger count cellranger aggr cellranger reanalyze cellranger mat2csv cellranger mkgtf cellranger mkref cellranger vdj cellranger mkvdjref cellranger testrun cellranger upload cellranger sitecheck

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Question: How does cellranger count auto-detect the assay chemistry? Answer: To auto-detect the assay chemistry (--chemistry=auto), cellranger count maps the first 10,000 reads in the FASTQ files. The 3' versus 5' assay configurations are inferred based on the dominant orientation of the R2 read mapping (from at least 1,000 mapped reads).

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Description of cellranger can be found here. 10X Genomics cellranger uses the STAR aligner under the hood to map reads to a genome after first preprocessing them (extracting cell and UMI sequences). cellranger version 3 has many sub-applications. cellranger mkfastq. cellranger count; cellranger aggr; cellranger reanalyze; cellranger mat2csv ...

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