DESCRIPTION.rst
LICENSE
MANIFEST.in
README.rst
setup.py
FUCHS/FUCHS.py
FUCHS/__init__.py
FUCHS/detect_skipped_exons.py
FUCHS/detect_splicing_variants.py
FUCHS/extract_reads.py
FUCHS/get_coverage_profile.py
FUCHS/get_mate_information.py
FUCHS/get_readnames_from_DCC.py
FUCHS/guided_denovo_circle_structure_parallel.py
FUCHS/permutate_motifs.py
FUCHS/proportion_of_fully_covered_circRNAs.py
FUCHS/replace_ids_with_names.py
FUCHS/write_fasta_for_fimo.py
FUCHS.egg-info/PKG-INFO
FUCHS.egg-info/SOURCES.txt
FUCHS.egg-info/dependency_links.txt
FUCHS.egg-info/entry_points.txt
FUCHS.egg-info/not-zip-safe
FUCHS.egg-info/requires.txt
FUCHS.egg-info/top_level.txt
data/gold/hek293_A.alternative_splicing.txt
data/gold/hek293_A.exon_counts.bed
data/gold/hek293_A.exon_counts.txt
data/gold/hek293_A.mate_status.txt
data/gold/hek293_A.skipped_exons.bed
data/gold/hek293_A.skipped_exons.txt
data/gold/hek293_B.alternative_splicing.txt
data/gold/hek293_B.exon_counts.bed
data/gold/hek293_B.exon_counts.txt
data/gold/hek293_B.mate_status.txt
data/gold/hek293_B.skipped_exons.bed
data/gold/hek293_B.skipped_exons.txt
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data/gold/hek293_B.coverage_profiles/cluster_association.all_circles.tsv
data/gold/hek293_B.coverage_profiles/cluster_association.long_circles.tsv
data/gold/hek293_B.coverage_profiles/cluster_association.medium_circles.tsv
data/gold/hek293_B.coverage_profiles/cluster_association.short_circles.tsv
data/gold/hek293_B.coverage_profiles/cluster_means.all_circles.tsv
data/gold/hek293_B.coverage_profiles/cluster_means.long_circles.tsv
data/gold/hek293_B.coverage_profiles/cluster_means.medium_circles.tsv
data/gold/hek293_B.coverage_profiles/cluster_means.short_circles.tsv
data/gold/hek293_B.coverage_profiles/coverage.clusters.all_circles.pdf
data/gold/hek293_B.coverage_profiles/coverage.clusters.long_circles.pdf
data/gold/hek293_B.coverage_profiles/coverage.clusters.medium_circles.pdf
data/gold/hek293_B.coverage_profiles/coverage.clusters.short_circles.pdf
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data/input/hek293_A.circIDs.txt
data/input/hek293_A.sorted.bam
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data/input/hek293_B.circIDs.txt
data/input/hek293_B.sorted.bam
data/input/hek293_B.sorted.bam.bai
data/input/hg38.RefSeq.exons.bed
data/output/hek293_A.alternative_splicing.txt 
data/output/hek293_A.exon_counts.bed
data/output/hek293_A.exon_counts.txt
data/output/hek293_A.mate_status.txt
data/output/hek293_A.skipped_exons.bed
data/output/hek293_A.skipped_exons.bed.sorted
data/output/hek293_A.skipped_exons.txt
data/output/hek293_B.alternative_splicing.txt 
data/output/hek293_B.exon_counts.bed
data/output/hek293_B.exon_counts.txt
data/output/hek293_B.mate_status.txt
data/output/hek293_B.skipped_exons.bed
data/output/hek293_B.skipped_exons.txt
data/output/hek293_A/1_15872816_15876678_9reads.sorted.bam
data/output/hek293_A/1_20749723_20773610_4reads.sorted.bam
data/output/hek293_A/1_8655973_8656441_5reads.sorted.bam
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data/output/hek293_B.coverage_profiles/4_185247294_185267155.NM_031953.txt
data/output/hek293_B.coverage_profiles/4_186706563_186709845.NM_005245.txt
data/output/hek293_B.coverage_profiles/4_1900626_1904378.NM_007331.txt
data/output/hek293_B.coverage_profiles/4_87046166_87047594.NM_005935.txt
data/output/hek293_B.coverage_profiles/4_87195324_87195690.NM_001292006.txt
data/output/hek293_B.coverage_profiles/5_123545417_123557564.NM_004384.txt
data/output/hek293_B.coverage_profiles/5_168488602_168494650.NM_002887.txt
data/output/hek293_B.coverage_profiles/5_178885614_178931326.NM_030613.txt
data/output/hek293_B.coverage_profiles/5_180261684_180280608.NM_001135044.txt
data/output/hek293_B.coverage_profiles/5_50399107_50411383.NM_198449.txt
data/output/hek293_B.coverage_profiles/5_65567513_65572286.NM_015342.txt
data/output/hek293_B.coverage_profiles/5_69174877_69175537.NM_031966.txt
data/output/hek293_B.coverage_profiles/5_74813840_74841679.NM_015566.txt
data/output/hek293_B.coverage_profiles/5_79439010_79457018.NM_004272.txt
data/output/hek293_B.coverage_profiles/5_94643273_94654752.NM_032290.txt
data/output/hek293_B.coverage_profiles/6_158282263_158314268.NM_020245.txt
data/output/hek293_B.coverage_profiles/6_158312051_158314268.NM_020245.txt
data/output/hek293_B.coverage_profiles/6_18236452_18258405.NM_003472.txt
data/output/hek293_B.coverage_profiles/6_47283938_47286595.NM_014452.txt
data/output/hek293_B.coverage_profiles/6_4891713_4892379.NM_001143970.txt
data/output/hek293_B.coverage_profiles/6_79042843_79060818.NM_017934.txt
data/output/hek293_B.coverage_profiles/7_100023419_100024307.NM_001287054.txt
data/output/hek293_B.coverage_profiles/7_122113118_122133741.NM_005763.txt
data/output/hek293_B.coverage_profiles/7_127373342_127377329.NM_176814.txt
data/output/hek293_B.coverage_profiles/7_135577796_135593192.NM_015135.txt
data/output/hek293_B.coverage_profiles/7_24623666_24668660.NM_001303037.txt
data/output/hek293_B.coverage_profiles/7_39987599_40002031.NM_031267.txt
data/output/hek293_B.coverage_profiles/8_127890589_127890998.NR_003367.txt
data/output/hek293_B.coverage_profiles/8_18765449_18804898.NM_015310.txt
data/output/hek293_B.coverage_profiles/9_135881633_135883078.NM_015447.txt
data/output/hek293_B.coverage_profiles/9_83678441_83686155.NM_053067.txt
data/output/hek293_B.coverage_profiles/9_85669485_85712566.NM_015239.txt
data/output/hek293_B.coverage_profiles/9_92256680_92269983.NM_002161.txt
data/output/hek293_B.coverage_profiles/X_131743096_131794466.NR_026975.txt
data/output/hek293_B.coverage_profiles/X_131749306_131785258.NR_026975.txt
data/output/hek293_B.coverage_profiles/X_131749306_131794466.NR_026975.txt
data/output/hek293_B.coverage_profiles/X_140783175_140784659.NM_004065.txt
data/output/hek293_B.coverage_profiles/X_14843660_14859334.NM_152633.txt
data/output/hek293_B.coverage_profiles/X_85247547_85270146.NM_021998.txt
data/output/hek293_B.coverage_profiles/cluster_association.all_circles.tsv
data/output/hek293_B.coverage_profiles/cluster_association.long_circles.tsv
data/output/hek293_B.coverage_profiles/cluster_association.medium_circles.tsv
data/output/hek293_B.coverage_profiles/cluster_association.short_circles.tsv
data/output/hek293_B.coverage_profiles/cluster_means.all_circles.tsv
data/output/hek293_B.coverage_profiles/cluster_means.long_circles.tsv
data/output/hek293_B.coverage_profiles/cluster_means.medium_circles.tsv
data/output/hek293_B.coverage_profiles/cluster_means.short_circles.tsv
data/output/hek293_B.coverage_profiles/coverage.clusters.all_circles.pdf
data/output/hek293_B.coverage_profiles/coverage.clusters.long_circles.pdf
data/output/hek293_B.coverage_profiles/coverage.clusters.medium_circles.pdf
data/output/hek293_B.coverage_profiles/coverage.clusters.short_circles.pdf
data/output/hek293_B.coverage_profiles/coverage_profiles.all_circles.pdf
scripts/FUCHS
scripts/guided_denovo_circle_structure_parallel
scripts/make_coverage_picture.R
scripts/summarized_coverage_profiles.R
scripts/summary_pictures.R