EI-CoreBioinformatics portcullis issues

EI-CoreBioinformatics / portcullis

Splice junction analysis and filtering from BAM files

https://ei-corebioinformatics.github.io/portcullis/

GNU General Public License v3.0

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issues

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Why would max_min_anc be larger than half of read length?

#66 ritetsu opened 1 month ago
0
terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value> >' ') for option '--input-file' is invalid

#65 pameyaw opened 1 year ago
0
I have two files that are not created when the command is restarting (portcullis.junctions.tab , portcullis.junctions.bed )

#64 sashulkaSh opened 1 year ago
0
ResolvePackageNotFound: python=3.1

#63 margaretwoodhouse opened 2 years ago
1
Using Portcullis on large Datasets in connection with Mikado

#62 cc-prolix opened 2 years ago
0
Compilation error with python 3.10

#61 dpryan79 opened 2 years ago
0
Portcullis junc detects no junctions if bam index file already present in bam dir

#60 OXB-DC opened 2 years ago
0
make fails

#59 francicco opened 2 years ago
2
terminate called after throwing an instance of 'boost::wrapexcept<portcullis::bam::BamException>'

#58 mezarque opened 3 years ago
0
JunctionException using portcullis junc

#57 cc-prolix closed 3 years ago
1
autogen.sh autoreconf ERROR

#56 francicco opened 4 years ago
1
UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment

#55 chnych closed 3 years ago
8
Handling differences between short and long reads

#54 LehmannN opened 4 years ago
4
could not open script file as a python file, any help with this error would be greatly appreciated. after brew install, portcullis full used

#53 trjojack opened 4 years ago
0
missed junction

#52 gorliver opened 4 years ago
0
more incorrect number of column errors

#51 adamfreedman opened 4 years ago
7
AttributeError: type object 'DataFrame' has no attribute 'from_csv'

#50 lijing28101 opened 4 years ago
9
portcullis::FileSystemError*

#49 Xiaofei-git opened 5 years ago
6
Read counts

#48 KMgoo opened 5 years ago
0
Exon is not exactly recognized

#47 KMgoo closed 5 years ago
12
An error during Filtering junctions

#46 KMgoo closed 5 years ago
12
Added library declaration to properly compile from source

#45 ghost closed 5 years ago
1
High Novel Splicce Junction Rate

#44 jgockley62 closed 5 years ago
6
problem w/ python missing dependency in source installation

#43 rdauria opened 5 years ago
3
error in portcullis bamfilt

#42 wenbinmei closed 5 years ago
13
Make portcullis work with long reads: ideas

#41 lucventurini opened 5 years ago
12
how does portcullis handle antisense reads?

#40 mparker2 closed 5 years ago
1
portcullis::JunctionError*

#39 lstxmu closed 5 years ago
4
[BUG] make check fails with conda python

#38 lucventurini closed 5 years ago
3
Parsing Command Line: too many positional options have been specified on the command line

#37 dfermin closed 5 years ago
1
[Singularity] Installation fails, even following instructions in the recipe in the Repo

#36 lucventurini closed 6 years ago
2
[BUG] Brew installation now broken after the release of Python 3.7

#35 lucventurini opened 6 years ago
1
conda conflicts with enum34?

#34 maximilianh closed 6 years ago
2
Using Portcullis on RHEL7

#33 beechwood13 closed 5 years ago
17
Streamline boost subset

#32 maplesond closed 5 years ago
1
Broken junctools convert due to changes in the tab format

#31 lucventurini closed 6 years ago
2
Counts of R1 and R2 for each strand

#30 maplesond closed 6 years ago
1
Ensure unique id after junctools set union

#29 maplesond opened 6 years ago
0
Added sort / reindex and prefix options to junctools set

#28 maplesond opened 6 years ago
0
Adapt initial positive set to sequencing depth and read length

#27 maplesond opened 7 years ago
1
Speed up rule based filtering

#26 maplesond closed 6 years ago
2
terminate called after throwing an instance of 'boost::exception_detail::clone_impl<portcullis::JunctionException>' what(): std::exception**

#25 fcamara7 closed 6 years ago
10
Investigate use of cross validation for selecting cutoff values.

#24 maplesond closed 5 years ago
1
Improve performance of rule-based filtering

#23 maplesond closed 7 years ago
2
Trouble starting with non-standard python3

#22 IanSudbery closed 8 years ago
4
Configure with python3

#21 colindaven closed 7 years ago
13
Define primary junctions

#20 lucventurini opened 8 years ago
0
Use score instead of coverage for the BED/GFF/GTF output

#19 lucventurini closed 7 years ago
2
[0.16.0] Portcullis filter dies as it cannot find the junction file

#18 lucventurini closed 8 years ago
5
Personalise GFF source field in the output

#17 lucventurini closed 8 years ago
1