YangLab CIRCexplorer2 issues

YangLab / CIRCexplorer2

circular RNA analysis toolset

http://circexplorer2.readthedocs.org/

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issues

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interpret circRNA coordinate

#75 frankligy opened 5 months ago
0
Reads per gene vs annotation file generated with CIRCexplorer2

#74 andre-gabriel-42 opened 7 months ago
0
Annotation with 0 fusions junctions (STAR alignment)

#73 andre-gabriel-42 opened 7 months ago
1
Annotation step with STAR data

#72 andre-gabriel-42 opened 7 months ago
0
circularRNA_known isoform and exons / outputs information

#71 npont opened 8 months ago
0
IndexError: list index out of range.

#70 jaberdehghani64 opened 10 months ago
2
Convert paired-end RNA-seq to single-read RNA-seq?

#69 junjunlab opened 10 months ago
3
Find circular RNA Fusion from Output of Annotate command

#68 manjumoorthy95 opened 1 year ago
0
Mitochondrial circRNAs with CIRCexploere2

#67 BirongZhang opened 1 year ago
1
why the CIRCexplorer2 is so slow

#66 z-bluesky opened 1 year ago
4
KeyError: '--cuff'

#65 shelkmike opened 1 year ago
3
Is CIRCexplorer2 allowing for STAR-generated bam file as input?

#64 lovebaboon1989 opened 1 year ago
1
want to use circexplorere2 for rat genome (Rnor_6.0)

#63 sharmi85 opened 1 year ago
1
What is hg19_ref_all.txt file?

#62 mathavanpu closed 3 months ago
3
CIRCexplorer2 parse

#61 muhammadharoon786 opened 2 years ago
0
Error in TopHat-Fusion

#60 smarhon closed 2 years ago
1
back_spliced_junctions.bed

#59 ericbrzoska opened 2 years ago
0
IndexError: list index out of range + CIRCexplorer2 parse

#58 BirongZhang closed 2 years ago
2
CIRCpedia download

#57 mumichae closed 2 years ago
1
skip comment lines of STAR chimeric output file

#56 gudeqing closed 2 years ago
1
Annoted 0 fusion junction

#55 JerryZhang-1222 closed 2 years ago
2
parse

#54 tanasa closed 2 years ago
2
refFlat file for solanum lycopersicum in the annotating step

#53 anuiranjan006 opened 3 years ago
1
CIRCexplorer2 parse Converted 0 fusion reads!

#52 JianGuoZhou3 opened 3 years ago
0
ValueError: too many values to unpack

#51 kopardev closed 3 years ago
1
Export backspliced junctions as separate bam file.

#50 kopardev opened 3 years ago
0
Python issues with parser and fetch_ucsc

#49 ryandikdan closed 3 years ago
1
ValueError while running align

#48 KasperThystrup closed 3 years ago
2
circRNA with only one base

#47 gudeqing closed 3 years ago
3
Fail to annotate MapSplice junctions

#46 BarryDigby closed 3 years ago
3
Does CIRCexplorer2 pipeline only works with mouse and human??

#45 sambhav2mishra closed 3 years ago
2
IndexError: list index out of range

#44 JianGuoZhou3 closed 3 years ago
5
fetch_ucsc hg38 kg

#43 BarryDigby closed 3 years ago
3
Unmapped BAM to single FASTQ (paired-end)

#42 anthfm closed 4 years ago
0
assemble module of CIRCexplorer2 keeps on running for around a week, is it a sign of error?

#41 sambhav2mishra closed 4 years ago
1
Invalid literal for int() with base 10: 'MIR6859-1

#40 CuypersBart closed 4 years ago
2
ValueError: need more than 2 values to unpack

#39 lliaokc closed 4 years ago
1
Is it possible to do circexplorer2 denovo using other aligners??

#38 sambhav2mishra closed 4 years ago
3
Not able to download mm10_ens.txt

#37 sambhav2mishra closed 4 years ago
1
Fix bug in ciRNA annotating

#36 kepbod closed 4 years ago
1
Error: cannot convert GenePred to GTF!

#35 sambhav2mishra closed 4 years ago
2
AttributeError: 'NoneType' object has no attribute 'group'

#34 sambhav2mishra closed 4 years ago
1
circularRNA_full.txt - confusing exonCount/exonSize/exonOffsets

#33 smahaffey closed 5 years ago
2
Issue with mm10_ens

#32 yzh37545 closed 5 years ago
2
Align unmapped reads from tophat2

#31 nedoluzhko closed 5 years ago
0
Parsing error

#30 smahaffey closed 5 years ago
4
Command for paired end data

#29 archu87 closed 5 years ago
4
Issue with fetch_uscs.py: TypeError

#28 Scathacheng closed 5 years ago
5
Analysis of Mitochondria

#27 andremrsantos closed 5 years ago
2
Error when multiple instances of CIRCexplorer2 annotate run from a same directory

#26 egaffo closed 5 years ago
1