YangLab/CIRCexplorer2 issues and pull requests

#75 - interpret circRNA coordinate

Issue - State: open - Opened by frankligy 9 months ago

#74 - Reads per gene vs annotation file generated with CIRCexplorer2

Issue - State: open - Opened by andre-gabriel-42 10 months ago

#73 - Annotation with 0 fusions junctions (STAR alignment)

Issue - State: open - Opened by andre-gabriel-42 11 months ago - 1 comment

#72 - Annotation step with STAR data

Issue - State: open - Opened by andre-gabriel-42 11 months ago

#71 - circularRNA_known isoform and exons / outputs information

Issue - State: open - Opened by npont 11 months ago

#70 - IndexError: list index out of range.

Issue - State: open - Opened by jaberdehghani64 about 1 year ago - 2 comments

#69 - Convert paired-end RNA-seq to single-read RNA-seq?

Issue - State: open - Opened by junjunlab about 1 year ago - 3 comments

#68 - Find circular RNA Fusion from Output of Annotate command

Issue - State: open - Opened by manjumoorthy95 over 1 year ago

#67 - Mitochondrial circRNAs with CIRCexploere2

Issue - State: open - Opened by BirongZhang over 1 year ago - 1 comment

#66 - why the CIRCexplorer2 is so slow

Issue - State: open - Opened by bakillersky over 1 year ago - 4 comments

#65 - KeyError: '--cuff'

Issue - State: open - Opened by shelkmike over 1 year ago - 3 comments

#64 - Is CIRCexplorer2 allowing for STAR-generated bam file as input?

Issue - State: open - Opened by lovebaboon1989 over 1 year ago - 1 comment

#63 - want to use circexplorere2 for rat genome (Rnor_6.0)

Issue - State: open - Opened by sharmi85 about 2 years ago - 1 comment

#62 - What is hg19_ref_all.txt file?

Issue - State: closed - Opened by mathavanpu about 2 years ago - 3 comments

#61 - CIRCexplorer2 parse

Issue - State: open - Opened by muhammadharoon786 over 2 years ago

#60 - Error in TopHat-Fusion

Issue - State: closed - Opened by smarhon over 2 years ago - 1 comment

#59 - back_spliced_junctions.bed

Issue - State: open - Opened by ericbrzoska over 2 years ago

#58 - IndexError: list index out of range + CIRCexplorer2 parse

Issue - State: closed - Opened by BirongZhang almost 3 years ago - 2 comments

#57 - CIRCpedia download

Issue - State: closed - Opened by mumichae about 3 years ago - 1 comment

#56 - skip comment lines of STAR chimeric output file

Issue - State: closed - Opened by gudeqing about 3 years ago - 1 comment

#55 - Annoted 0 fusion junction

Issue - State: closed - Opened by JerryZhang-1222 about 3 years ago - 2 comments

#54 - parse

Issue - State: closed - Opened by tanasa about 3 years ago - 2 comments

#53 - refFlat file for solanum lycopersicum in the annotating step

Issue - State: open - Opened by anuiranjan006 over 3 years ago - 1 comment

#52 - CIRCexplorer2 parse Converted 0 fusion reads!

Issue - State: open - Opened by jianguozhouzunyimedicaluniversity over 3 years ago

#51 - ValueError: too many values to unpack

Issue - State: closed - Opened by kopardev over 3 years ago - 1 comment

#50 - Export backspliced junctions as separate bam file.

Issue - State: open - Opened by kopardev almost 4 years ago

#49 - Python issues with parser and fetch_ucsc

Issue - State: closed - Opened by ryandikdan almost 4 years ago - 1 comment

#48 - ValueError while running align

Issue - State: closed - Opened by KasperThystrup about 4 years ago - 2 comments

#47 - circRNA with only one base

Issue - State: closed - Opened by gudeqing about 4 years ago - 3 comments

#46 - Fail to annotate MapSplice junctions

Issue - State: closed - Opened by BarryDigby about 4 years ago - 3 comments

#45 - Does CIRCexplorer2 pipeline only works with mouse and human??

Issue - State: closed - Opened by sambhav2mishra about 4 years ago - 2 comments

#44 - IndexError: list index out of range

Issue - State: closed - Opened by jianguozhouzunyimedicaluniversity about 4 years ago - 5 comments

#43 - fetch_ucsc hg38 kg

Issue - State: closed - Opened by BarryDigby about 4 years ago - 3 comments

#42 - Unmapped BAM to single FASTQ (paired-end)

Issue - State: closed - Opened by anthfm over 4 years ago

#41 - assemble module of CIRCexplorer2 keeps on running for around a week, is it a sign of error?

Issue - State: closed - Opened by sambhav2mishra over 4 years ago - 1 comment

#40 - Invalid literal for int() with base 10: 'MIR6859-1

Issue - State: closed - Opened by CuypersBart over 4 years ago - 2 comments

#39 - ValueError: need more than 2 values to unpack

Issue - State: closed - Opened by lliaokc almost 5 years ago - 1 comment

#38 - Is it possible to do circexplorer2 denovo using other aligners??

Issue - State: closed - Opened by sambhav2mishra about 5 years ago - 3 comments

#37 - Not able to download mm10_ens.txt

Issue - State: closed - Opened by sambhav2mishra about 5 years ago - 1 comment

#36 - Fix bug in ciRNA annotating

Pull Request - State: closed - Opened by kepbod about 5 years ago - 1 comment

#35 - Error: cannot convert GenePred to GTF!

Issue - State: closed - Opened by sambhav2mishra about 5 years ago - 2 comments

#34 - AttributeError: 'NoneType' object has no attribute 'group'

Issue - State: closed - Opened by sambhav2mishra about 5 years ago - 1 comment

#33 - circularRNA_full.txt - confusing exonCount/exonSize/exonOffsets

Issue - State: closed - Opened by smahaffey over 5 years ago - 2 comments

#32 - Issue with mm10_ens

Issue - State: closed - Opened by yzh37545 over 5 years ago - 2 comments

#31 - Align unmapped reads from tophat2

Issue - State: closed - Opened by nedoluzhko over 5 years ago

#30 - Parsing error

Issue - State: closed - Opened by smahaffey over 5 years ago - 4 comments

#29 - Command for paired end data

Issue - State: closed - Opened by archu87 over 5 years ago - 4 comments

#28 - Issue with fetch_uscs.py: TypeError

Issue - State: closed - Opened by Scathacheng over 5 years ago - 5 comments

#27 - Analysis of Mitochondria

Issue - State: closed - Opened by andremrsantos over 5 years ago - 2 comments

#26 - Error when multiple instances of CIRCexplorer2 annotate run from a same directory

Issue - State: closed - Opened by egaffo almost 6 years ago - 1 comment

#25 - Changes required for Python 3.x compatibility

Pull Request - State: closed - Opened by lardenoije almost 6 years ago - 2 comments

#24 - AS detection error in CIRCExxplorer2 devono?

Issue - State: closed - Opened by tw7649116 about 6 years ago - 2 comments

#23 - Questions in parsing tophat-fusion mapping results with stranded RNA-seq

Issue - State: closed - Opened by broadax about 6 years ago

#22 - IndexError: list index out of range

Issue - State: closed - Opened by ghost about 6 years ago - 4 comments

#21 - Idea about using STAR Chimeric.out.junction file for circRNA alternative splicing analysis

Issue - State: closed - Opened by kepbod about 6 years ago - 1 comment

#20 - a question about align

Issue - State: closed - Opened by weishuxun about 6 years ago - 1 comment

#19 - Is it possible to use assemble function with STAR output?

Issue - State: closed - Opened by qoiopipq over 6 years ago - 1 comment

#18 - Apparent problem with pybedtools binaries after PIP download

Issue - State: closed - Opened by illWill over 6 years ago - 1 comment

#17 - Issues with fetch_ucsc.py

Issue - State: closed - Opened by harshameghadri over 6 years ago - 1 comment

#16 - CIRCexplorer2 support hisat2

Issue - State: closed - Opened by weizhiting over 6 years ago - 6 comments

#15 - gtf to txt conversion

Issue - State: closed - Opened by tut3 almost 7 years ago - 1 comment

#14 - Deal with last comma of exonStarts and exonEnds

Issue - State: closed - Opened by Tong-Chen almost 7 years ago - 1 comment

#13 - No module named dir_func

Issue - State: closed - Opened by maojn almost 7 years ago - 1 comment

#12 - ImportError: libbz2.so.1.0: cannot open shared object file: No such file or directory

Issue - State: closed - Opened by maojn about 7 years ago

#11 - Annotate ouput

Issue - State: closed - Opened by zoewardnz about 7 years ago - 1 comment

#10 - support python 3

Pull Request - State: closed - Opened by kepbod about 7 years ago - 4 comments

GitHub / YangLab/CIRCexplorer2 issues and pull requests