Test data¶
Download test dataset¶
Test dataset can be downloaded from Github.
wget https://github.com/Kevinzjy/CIRIquant/releases/download/v0.2.0/test_data.tar.gz
tar zxvf test_data.tar.gz
circRNA quantification¶
Folder quant
contain the test dataset for circRNA quantification.
1. Generate hisat2 and bwa index¶
cd ./test_data/quant
bwa index -a bwtsw -p chr1.fa chr1.fa
hisat2-build ./chr1.fa ./chr1.fa
2. Customize the configuration¶
Replace the path of bwa
/hisat2
/stringtie
/samtools
in chr1.yml
with your own version.
3. Run test dataset¶
Test data set can be retrived under test_data/quant
folder, you can replace the path of required software in the chr1.yml
with your own version
CIRIquant -t 4 \
-1 ./test_1.fq.gz \
-2 ./test_2.fq.gz \
--config ./chr1.yml \
--no-gene \
-o ./test \
-p test
The demo dataset should take approximately 5 minutes on a personal computer. It has been tested on my PC with Intel i7-8700 processor and 16G of memory, running Ubuntu 18.04 LTS.
The structure of output directory ./test
should be like this:
test
├── align
│ ├── test.bam
│ ├── test.sorted.bam
│ └── test.sorted.bam.bai
├── circ
│ ├── test.ciri
│ ├── test.ciri.bed
│ ├── test_denovo.bam
│ ├── test_denovo.sorted.bam
│ ├── test_denovo.sorted.bam.bai
│ ├── test_index.1.ht2
│ ├── test_index.2.ht2
│ ├── test_index.3.ht2
│ ├── test_index.4.ht2
│ ├── test_index.5.ht2
│ ├── test_index.6.ht2
│ ├── test_index.7.ht2
│ ├── test_index.8.ht2
│ ├── test_index.fa
│ └── test_unmapped.sam
├── CIRIerror.log
├── test.bed
├── test.gtf
└── test.log
Then, you can check the main output in ./test/test.gtf
.
Differential expression analysis¶
Folder DE
contain the test dataset for differential expression analysis
cd ./test_data/DE
# Test for DE-score and DS-score calculation
CIRI_DE -n ctrl.gtf \
-c case.gtf \
-o CIRI_DE.tsv
# Test for RNase R correction
CIRI_DE -n ctrl_corrected.gtf \
-c case_corrected.gtf \
-o CIRI_DE_corrected.tsv