circRIP: An accurate tool for identifying circRNA-RBP interaction
pysam (0.14.1)
pandas (1.0.3)
featureCounts (v1.6.1)
gtfToGenePred
bedtools (v2.26.0)
STAR (2.7.5a)
bowtie2 (2.4.2)
circRIP identify circRNA by parsing STAR mapping results and re-mapping the unmapped reads to known circRNA back-splice junctions(BSJs)
requisited input files:
test_ip_1.fq.gz,test_ip_2.fq.gz,test_input_1.fq.gz,test_input_2.fq.gz fastq files of IP/Input
~/starindex/ the STAR index
~/bowtie2index/circBase the bowtie2 index of circRNA junctions
gencode.v32.annotation.gtf the GTF format gene annotation
GRCh38.p10.genome.fa the genome fasta file
command lines:
# IP
python circRIP.py circRNAIdentify -fq1 test_ip_1.fq.gz -fq2 test_ip_2.fq.gz \
-star_index ~/starindex/ -bowtie2_index ~/bowtie2index/circBase \
-p 30 -gtf gencode.v32.annotation.gtf -genome GRCh38.p10.genome.fa -prefix test_ip.circ -junLen 100
# Input
python circRIP.py circRNAIdentify -fq1 test_input_1.fq.gz -fq2 test_input_2.fq.gz \
-star_index ~/starindex/ -bowtie2_index ~/bowtie2index/circBase \
-p 30 -gtf gencode.v32.annotation.gtf -genome GRCh38.p10.genome.fa -prefix test_input.circ -junLen 100
results:
the column of test_ip/input.circ is:
1, Chromosome
2, circRNA start coordinates
3, circRNA end coordinates
4, circRNA BSJs reads counts
Users are free to use the circRNA recognition software, as long as the following conditions are met:
1, transform the results to four columns format as described above.
2, bam files of linear reads(to detecte forward-splice junctions, splice-aware aligners such as STAR should be used to perform reads mapping)
circRIP identify IP-enriched circRNA by c-test:
requisited input files:
test_ip.circ/test_input.circ circRNAs in four columns format
test_ip.circAligned.out.bam/test_input.circAligned.out.bam bam files of linear reads
gencode.v32.annotation.gtf the GTF format gene annotation
GRCh38.p10.genome.fa the genome fasta file
command lines:
python circRIP.py EnrichedcircRNA -ip_circ test_ip.circ -input_circ test_input.circ -gtf gencode.v32.annotation.gtf \
-ip_bam test_ip.circAligned.out.bam -input_bam test_input.circAligned.out.bam -prefix test.final.out \
-G GRCh38.p10.genome.fa
results:
circRIP generates two output files test.final.out and test.final.out.html, test.final.out is the txt format results and test.final.out.html is a web report page
the column of test.final.out is:
1, circRNA ID(Chromosome:start|end)
2, circRNA host gene symbol
3, circRNA BSJs in IP
4, circRNA BSJs in Input
5, circRNA CPM in IP
6, circRNA CPM in Input
7, IP/Input ratio
8, P value
9, circRNA status (enriched or non-enriched)
test.final.out.html: