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 下載基因組序列和基因組注釋文件
大鼠基因組和注釋文件：
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
登錄計(jì)算節(jié)點(diǎn)斥季，激活環(huán)境
salloc -p tyhctest -N 1 -n 2
ssh 計(jì)算節(jié)點(diǎn)
source ~/miniconda3/bin/activate
conda activate celescope
過(guò)濾非編碼基因
celescope utils mkgtf Rattus_norvegicus.mRatBN7.2.109.gtf Rattus_norvegicus.filter.gtf
提交任務(wù)
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
退出計(jì)算節(jié)點(diǎn)
logout#或者Ctrl + D
參考資料：
GEXSCOPE?單細(xì)胞(核)轉(zhuǎn)錄組數(shù)據(jù)分析-新格元生物科技 (singleronbio.com)
