.coveragerc
.gitignore
.travis.yml
CHANGELOG.md
LICENSE.txt
README.md
README.rst
mkdocs.yml
requirements.txt
setup.cfg
setup.py
CIRCexplorer2.egg-info/PKG-INFO
CIRCexplorer2.egg-info/SOURCES.txt
CIRCexplorer2.egg-info/dependency_links.txt
CIRCexplorer2.egg-info/entry_points.txt
CIRCexplorer2.egg-info/pbr.json
CIRCexplorer2.egg-info/requires.txt
CIRCexplorer2.egg-info/top_level.txt
circ2/__init__.py
circ2/align.py
circ2/annotate.py
circ2/assemble.py
circ2/command_parse.py
circ2/denovo.py
circ2/dir_func.py
circ2/fetch_ucsc.py
circ2/genomic_interval.py
circ2/helper.py
circ2/parse.py
circ2/parser.py
circ2/version.py
docs/index.md
docs/about/changelog.md
docs/about/faq.md
docs/about/license.md
docs/about/tools.md
docs/image/annotating_pipeline.jpg
docs/image/characterization_pipeline.jpg
docs/modules/align.md
docs/modules/annotate.md
docs/modules/assemble.md
docs/modules/denovo.md
docs/modules/parse.md
docs/tutorial/alignment.md
docs/tutorial/annotating.md
docs/tutorial/as.md
docs/tutorial/assembly.md
docs/tutorial/pipeline.md
docs/tutorial/setup.md
test/__init__.py
test/test_annotate.py
test/test_denovo.py
test/test_parse.py
test/utils.py
test/data/Chimeric.out.junction
test/data/RNA_seq_bwa.sam
test/data/chr21.fa
test/data/chr21.fa.fai
test/data/fusion_junction.bed
test/data/fusions_raw.txt
test/data/ref.txt
test/data/splicesites.bed
test/data/tophat_fusion.bam
test/data/BWA_out/fusion_junction.bed
test/data/MapSplice_out/fusion_junction.bed
test/data/STAR_out/fusion_junction.bed
test/data/TopHat_Fusion_out/fusion_junction.bed
test/data/annotate_result/annotated_fusion.txt
test/data/annotate_result/circ_fusion.txt
test/data/cufflinks/transcripts_ref.txt
test/data/denovo_result/all_exon_info.txt
test/data/denovo_result/annotated_circ.txt
test/data/denovo_result/annotated_fusion.txt
test/data/denovo_result/circ_fusion.txt
test/data/denovo_result/combined_ref.txt
test/data/denovo_result/novel_circ.txt
test/data/pAplus_tophat/junctions.bed
test/data/segemehl_out/fusion_junction.bed
test/data/tophat/junctions.bed