使用方法

celescope rna mkref --help

usage: celescope rna mkref [-h] [--thread THREAD] --genome_name GENOME_NAME [--dry_run] --fasta FASTA [--STAR_param STAR_PARAM] --gtf GTF
                           [--mt_gene_list MT_GENE_LIST] [--attributes ATTRIBUTES]

optional arguments:
  -h, --help            show this help message and exit
  --thread THREAD       Default=6. Threads to use. (default: 6)
  --genome_name GENOME_NAME
                        Required, genome name.  (default: None)
  --dry_run             Only write config file and exit. (default: False)
  --fasta FASTA         Required. fasta file name. (default: None)
  --STAR_param STAR_PARAM
                        Additional parameters for the called software. Need to be enclosed in quotation marks. For example, `--{software}_param "--param1 value1 --param2 value2"`. (default: )
  --gtf GTF             Required. Gtf file name. (default: None)
  --mt_gene_list MT_GENE_LIST
                        Mitochondria gene list file name. This file is a plain text file with one gene per line. 
                        If not provided, will use `MT-` and `mt-` to determine mitochondria genes. (default: None)
  --attributes ATTRIBUTES
                        Attributes to keep. Example: `gene_biotype=protein_coding,lncRNA,antisense;` (default: gene_biotype=protein_coding,lncRNA,antisense,IG_LV_gene,IG_V_gene,IG_V_pseudogene,IG_D_gene,IG_J_gene,IG_J_pseudogene,IG_C_gene,IG_C_pseudogene,TR_V_gene,TR_V_pseudogene,TR_D_gene,TR_J_gene,TR_J_pseudogene,TR_C_gene;)

1 下载基因组序列和基因组注释文件

大鼠基因组和注释文件：
Rattus_norvegicus - Ensembl genome browser 105

wget -c https://ftp.ensembl.org/pub/release-112/fasta/rattus_norvegicus/dna/Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa.gz

wget -c http://ftp.ensembl.org/pub/release-104/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.104.gtf.gz

登录计算节点，激活环境

salloc -p tyhctest -N 1 -n 2
ssh 计算节点
source ~/miniconda3/bin/activate
conda activate celescope

过滤非编码基因

celescope utils mkgtf Rattus_norvegicus.mRatBN7.2.109.gtf Rattus_norvegicus.filter.gtf

提交任务

source ~/miniconda3/bin/activate
conda activate celescope
celescope rna mkref \
--thread 64 \
--genome_name Rat \
--fasta /work/home/acwnw4bl7y/Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa \
--gtf /work/home/acwnw4bl7y/Rattus_norvegicus.filter.gtf

退出计算节点

logout#或者Ctrl + D

参考资料：

GEXSCOPE®单细胞(核)转录组数据分析-新格元生物科技 (singleronbio.com)