RNA velocity | RNA速率 | velocyto教程

一个比原版更好用的RNA velocity分析工具：velocyto

GitHub：https://github.com/velocyto-team/velocyto.R

readthedoc：http://velocyto.org/velocyto.py/index.html

历史分析参考：

project/scRNA-seq/velocyto - for smart-seq data

project/scRNA-seq/rawData/smart-seq/analysis/velocyto - for smart-seq data

project/scRNA-seq/rawData/10x/Jun_2020/analysis/velocyto - for 10x Genomics data

project/scPipeline/human/Human-Organoid/PHOX2B-Organoid-BO1/VelocityBasics.ipynb - NB

需要1一个bam文件和2个注释文件

-m, --mask FILE                 .gtf file containing intervals to mask
GTFFILE

注意注释文件有人和鼠的区别，均需要与cellranger处理时用的注释文件版本一致。

10x的数据处理非常简单，一行命令即可搞定。

velocyto run10x -m ensembl/release91/GRCh38_rmsk.gtf project/scRNA-seq/rawData/10x/Jun_2020/analysis/7Ala-D60-BO_report cellranger_ref/2019_Aug/refdata-cellranger-GRCh38-3.0.0/genes/genes.gtf

smart-seq的数据处理现在也变简单了，一行命令搞定。

velocyto run-smartseq2 -o OUTPUT -m databases/hg19/hg19_rmsk.gtf -e HSCR bam.link.2650/*.bam databases/hg19/gencode.v27.annotation.gtf

分析经验：

首先要检验bam文件的完整性，不然肯定会报错；

其次就是要大致知道运行时间，2500左右的细胞大概要运行80个小时；

Job information and usage summary of your CGS-HPCF job 689116 :
+--------------+----------+-------+----------+------+---------------------+-----------+------+------+
| jobid        | username | queue | jobname  | E S  | End Time            | walltime% | mem% | cpu% |
+--------------+----------+-------+----------+------+---------------------+-----------+------+------+
| 689116.omics | lizhixin | large | velocyto |    0 | 2021-01-16 07:13:21 |     94.98 | 7.95 | 8.32 |
+--------------+----------+-------+----------+------+---------------------+-----------+------+------+
+---------------------+---------------------+----------+----------+------+-------------+-------+----------+--------+
| Submit Time         | Start Time          | wtime@   | wtime#   | mem@ | mem#        | vmem@ | CPUTime@ | nproc# |
+---------------------+---------------------+----------+----------+------+-------------+-------+----------+--------+
| 2021-01-12 23:06:51 | 2021-01-12 23:26:26 | 79:46:55 | 84:00:00 | 7.95 | 104857600kb | 10.38 | 79:39:54 |     12 |
+---------------------+---------------------+----------+----------+------+-------------+-------+----------+--------+
+-------------+
| hostlist    |
+-------------+
| hpch06/1*12 |
+-------------+
E S = Exit Status ; % = usage percentage; # = requested ; @ = used ; mem@/vmem@ in GB ; nproc = number of processors

结果图：

RNA velocity | RNA速率 | velocyto教程　