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