毕业设计记录——全转录组分析（3）ciriRNA-seq上游分析

#安装ciriquant，参考https://ciri-cookbook.readthedocs.io/en/latest/CIRIquant_5_test.html#circrna-quantification
##创建environment.yml，内容如下
name: cirirna
channels:
- defaults
- bioconda
- conda-forge
dependencies:
- bioconda::bwa=0.7.17
- bioconda::hisat2=2.2.0
- bioconda::stringtie=2.1.1
- bioconda::samtools>=1.10
- bioconda::bioconductor-edger=3.28.0
- bioconda::bioconductor-limma=3.42.0
- conda-forge::r-statmod=1.4.35
- conda-forge::r-base=3.6
- conda-forge::r-optparse=1.6.6
- python=2.7.15
- pip=20.0.2
- perl=5.26.2
- pip:
  - CIRIquant>=1.1.2
  - numexpr==2.6.9
  - numpy==1.16.4
  - pysam==0.15.2
  - PyYAML==5.4
  - scikit-learn==0.20.3
  - scipy==1.2.2
  - argparse>=1.2.1
##然后运行
cd /home/zcc2023/mouse/circrna
nohup conda env create -f environment.yml &
conda activate cirirna

#建立索引
cd /home/zcc2023/mouse/index
nohup bwa index -a bwtsw -p GRCm38.fa GRCm38.fa &
nohup hisat2-build ./GRCm38.fa ./GRCm38.fa &

##.yml为参数文件
cd /home/zcc2023/mouse/circrna
nohup CIRIquant -t 40 -1 /home/zcc2023/mouse/seq/Mouse_T823-01-L01_good_1.fq.gz -2 /home/zcc2023/mouse/seq/Mouse_T823-01-L01_good_2.fq.gz --config ./test.yml -o /home/zcc2023/mouse/circrna/ -p Mouse_T823-01-L01 &
nohup CIRIquant -t 40 -1 /home/zcc2023/mouse/seq/Mouse_T823-01-L02_good_1.fq.gz -2 /home/zcc2023/mouse/seq/Mouse_T823-01-L02_good_2.fq.gz --config ./test.yml -o /home/zcc2023/mouse/circrna/ -p Mouse_T823-01-L02 &
nohup CIRIquant -t 40 -1 /home/zcc2023/mouse/seq/Mouse_T823-01-L03_good_1.fq.gz -2 /home/zcc2023/mouse/seq/Mouse_T823-01-L03_good_2.fq.gz --config ./test.yml -o /home/zcc2023/mouse/circrna/ -p Mouse_T823-01-L03 &
nohup CIRIquant -t 40 -1 /home/zcc2023/mouse/seq/Mouse_T823-01-L04_good_1.fq.gz -2 /home/zcc2023/mouse/seq/Mouse_T823-01-L04_good_2.fq.gz --config ./test.yml -o /home/zcc2023/mouse/circrna/ -p Mouse_T823-01-L04 &

test.yml示例如下
name: GRCm38
tools:
  bwa: /home/zcc2023/miniconda3/envs/cirirna/bin/bwa
  hisat2: /home/zcc2023/miniconda3/envs/cirirna/bin/hisat2
  stringtie: /home/zcc2023/miniconda3/envs/cirirna/bin/stringtie
  samtools: /home/zcc2023/miniconda3/envs/cirirna/bin/samtools

reference:
  fasta: /home/zcc2023/mouse/index/GRCm38.fa
  gtf: /home/zcc2023/mouse/index/GRCm38.gtf
  bwa_index: /home/zcc2023/mouse/index/GRCm38.fa
  hisat_index: /home/zcc2023/mouse/index/GRCm38.fa

##得到的文件没有结果.gtf文件，用下载好的Hisat2重新跑一遍试试

#cirirna拼错了，重新做一遍，重复的都不重做了
#软件前面安装好了，改一下test.yml文件内容，Hisat索引改为下载好的，然后重新跑
cd /home/zcc2023/mouse/cirirna
nohup CIRIquant -t 40 -1 /home/zcc2023/mouse/seq/Mouse_T823-01-L01_good_1.fq.gz -2 /home/zcc2023/mouse/seq/Mouse_T823-01-L01_good_2.fq.gz --config ./test.yml -o /home/zcc2023/mouse/cirirna/ -p Mouse_T823-01-L01 &
nohup CIRIquant -t 40 -1 /home/zcc2023/mouse/seq/Mouse_T823-01-L02_good_1.fq.gz -2 /home/zcc2023/mouse/seq/Mouse_T823-01-L02_good_2.fq.gz --config ./test.yml -o /home/zcc2023/mouse/cirirna/ -p Mouse_T823-01-L02 &
nohup CIRIquant -t 40 -1 /home/zcc2023/mouse/seq/Mouse_T823-01-L03_good_1.fq.gz -2 /home/zcc2023/mouse/seq/Mouse_T823-01-L03_good_2.fq.gz --config ./test.yml -o /home/zcc2023/mouse/cirirna/ -p Mouse_T823-01-L03 &
nohup CIRIquant -t 40 -1 /home/zcc2023/mouse/seq/Mouse_T823-01-L04_good_1.fq.gz -2 /home/zcc2023/mouse/seq/Mouse_T823-01-L04_good_2.fq.gz --config ./test.yml -o /home/zcc2023/mouse/cirirna/ -p Mouse_T823-01-L04 &

test.yml示例如下
name: GRCm38
tools:
  bwa: /home/zcc2023/miniconda3/envs/cirirna/bin/bwa
  hisat2: /home/zcc2023/miniconda3/envs/cirirna/bin/hisat2
  stringtie: /home/zcc2023/miniconda3/envs/cirirna/bin/stringtie
  samtools: /home/zcc2023/miniconda3/envs/cirirna/bin/samtools

reference:
  fasta: /home/zcc2023/mouse/index/GRCm38.fa
  gtf: /home/zcc2023/mouse/index/GRCm38.gtf
  bwa_index: /home/zcc2023/mouse/index/GRCm38.fa
  hisat_index: /home/zcc2023/mouse/index/grcm38/genome