<![CDATA[单细胞分析pipeline设计与验证]]>1.软件安装
cell ranger 6.1

curl -o cellranger-6.1.0.tar.gz "https://cf.10xgenomics.com/releases/cell-exp/cellranger-6.1.0.tar.gz?Expires=1628798968&Policy=eyJTdGF0ZW1lbnQiOlt7IlJlc291cmNlIjoiaHR0cHM6Ly9jZi4xMHhnZW5vbWljcy5jb20vcmVsZWFzZXMvY2VsbC1leHAvY2VsbHJhbmdlci02LjEuMC50YXIuZ3oiLCJDb25kaXRpb24iOnsiRGF0ZUxlc3NUaGFuIjp7IkFXUzpFcG9jaFRpbWUiOjE2Mjg3OTg5Njh9fX1dfQ__&Signature=IDnv8TCqfkxaEFEt3c6rwO~dWltlWa5Kr5b-CQeOgGMFjmVYwWVCLZ1pEKnoncD8waXaUj9gCNIChyDjS-nETYLwSEK~n1JkEUkjYZwLhPjKWlG87BEIjT1WORM4SotaaC2Vys5QvgBZh1YOh5VqqEJygpUFRMd0dNHTi0BXPFVk44iGhb~qXwvjIIpfogcbljZ~ytF5AsQv387VL4qRvlmhsGkApaNmWLwsBD9RdEwLEbQ3z4QaBCtI9lKHqduU-TF-b4~HNutYuniNWlVf9NjrdJngsYTS-0fY-CoKQeJb9ZZ8S5n6~wKsPdAtjrxfWKOEXAdmrw5-HHySE7fVuQ__&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA"
$ cd /opt
[ download file from downloads page ]
$ tar -xzvf cellranger-6.1.0.tar.gz

下载参考基因组

curl -O https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2020-A.tar.gz
$ tar -xzvf refdata-gex-GRCh38-2020-A.tar.gz

下载bcl2fastq
https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html

bcl2fastq_letterbooklet_15038058brpmi.pdf
进入 src
./configure & make & make install

]]>http://an.forum.genostack.com/topic/383/单细胞分析pipeline设计与验证RSS for NodeSat, 13 Jun 2026 09:38:33 GMTThu, 12 Aug 2021 08:28:36 GMT60<![CDATA[Reply to 单细胞分析pipeline设计与验证 on Fri, 13 Aug 2021 02:54:28 GMT]]>https://bioinformatics.stackexchange.com/questions/4271/what-is-cellranger-doing-in-comparison-to-other-methods

cell ranger 其实是一个pipeline 内部也调用了 star 这些软件 我们其实可以把这个pipeline 打开 做成一个通用而且可以调整的流程 类似于DropSeq
考虑到 cell ranger 只能支持10X的实验数据 大家已经意识到这个问题了 未来估计会出现一个通用的流程 ：
https://www.biorxiv.org/content/10.1101/2020.02.09.940221v1.full

]]>http://an.forum.genostack.com/post/754http://an.forum.genostack.com/post/754Fri, 13 Aug 2021 02:54:28 GMT<![CDATA[Reply to 单细胞分析pipeline设计与验证 on Fri, 13 Aug 2021 03:08:15 GMT]]>计算 count

wget https://cf.10xgenomics.com/samples/cell-exp/3.0.0/pbmc_1k_v3/pbmc_1k_v3_fastqs.tar

--id 会根据这个id创建运行临时输出目录

output有多种输出格式
47247183-c558-4bcd-9a90-b59758e5889d-image.png
咱们比较适合用原始的矩阵
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices

]]>http://an.forum.genostack.com/post/753http://an.forum.genostack.com/post/753Fri, 13 Aug 2021 03:08:15 GMT<![CDATA[Reply to 单细胞分析pipeline设计与验证 on Thu, 12 Aug 2021 12:33:45 GMT]]>cellranger mkfastq --help

There are three arguments or inputs that are added to the cellranger mkfastq command: –-id, --run, and --csv.

The --id can be anything. It is used by the pipeline to name the output directory that Cell Ranger is going to create to run in. This directory is called a pipestance, which is short for pipeline instance.

The --run argument points to the Illumina run folder that contains the BCL files.

The --csv argument is a comma-separated values (CSV) file that describes how samples were indexed on the Illumina flow cell.

cellranger mkfastq --id=tutorial_walk_through \
--run=/mnt/home/user.name/yard/run_cellrnager_mkfastq/cellranger-tiny-bcl-1.2.0 \
--csv=/mnt/home/user.name/yard/run_cellrnager_mkfastq/cellranger-tiny-bcl-simple-1.2.0.csv
]]>http://an.forum.genostack.com/post/751http://an.forum.genostack.com/post/751Thu, 12 Aug 2021 12:33:45 GMT<![CDATA[Reply to 单细胞分析pipeline设计与验证 on Thu, 12 Aug 2021 09:37:53 GMT]]>n file included from /ceph_disk3/single_cell/bcl2fastq/src/cxx/include/common/Debug.hh:22:0,
from /ceph_disk3/single_cell/bcl2fastq/src/cxx/lib/common/InstallationPath.cpp:22:
/ceph_disk3/single_cell/bcl2fastq/src/cxx/lib/common/InstallationPath.cpp: In constructor ‘bcl2fastq::common::InstallationPath::InstallationPath()’:
/ceph_disk3/single_cell/bcl2fastq/src/cxx/include/common/Logger.hh:38:14: error: ‘clog’ is not a member of ‘std’

vi /ceph_disk3/single_cell/bcl2fastq/src/cxx/include/common/Logger.hh

在头文件添加 #include <iostream>

/ceph_disk3/single_cell/bcl2fastq/src/cxx/lib/io/Xml.cpp:175:104: error: no matching function for call to ‘xml_writer_make_settings(char, int)’
boost::property_tree::write_xml(os, tree, boost::property_tree::xml_writer_make_settings(' ', 2));
https://gist.github.com/moonwatcher/ac1176971d6032fc9e0d4402e5a81333

]]>http://an.forum.genostack.com/post/749http://an.forum.genostack.com/post/749Thu, 12 Aug 2021 09:37:53 GMT