EI-CoreBioinformatics/portcullis

Issues

• Why would max_min_anc be larger than half of read length?

  #66 opened 4 months ago by ritetsu
  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 opened 2 years ago by pameyaw
  0

• I have two files that are not created when the command is restarting (portcullis.junctions.tab , portcullis.junctions.bed )

  #64 opened 2 years ago by sashulkaSh
  0

• ResolvePackageNotFound: python=3.1

  #63 opened 2 years ago by margaretwoodhouse
  1

• Using Portcullis on large Datasets in connection with Mikado

  #62 opened 2 years ago by cc-prolix
  0

• Compilation error with python 3.10

  #61 opened 2 years ago by dpryan79
  0

• Portcullis junc detects no junctions if bam index file already present in bam dir

  #60 opened 3 years ago by OXB-DC
  0

• make fails

  #59 opened 3 years ago by francicco
  2

• terminate called after throwing an instance of 'boost::wrapexcept<portcullis::bam::BamException>'

  #58 opened 4 years ago by mezarque
  0

• JunctionException using portcullis junc

  #57 opened 4 years ago by cc-prolix
  1

• portcullis::FileSystemError*

  #49 opened 5 years ago by Xiaofei-git
  6

• UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment

  #55 opened 4 years ago by chnych
  8

• problem w/ python missing dependency in source installation

  #43 opened 6 years ago by rdauria
  3

• autogen.sh autoreconf ERROR

  #56 opened 5 years ago by francicco
  1

• AttributeError: type object 'DataFrame' has no attribute 'from_csv'

  #50 opened 5 years ago by lijing28101
  9

• Handling differences between short and long reads

  #54 opened 5 years ago by LehmannN
  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 opened 5 years ago by trjojack
  0

• Using Portcullis on RHEL7

  #33 opened 6 years ago by beechwood13
  17

• missed junction

  #52 opened 5 years ago by gorliver
  0

• more incorrect number of column errors

  #51 opened 5 years ago by adamfreedman
  7

• portcullis::JunctionError*

  #39 opened 6 years ago by lstxmu
  4

• Read counts

  #48 opened 5 years ago by KMgoo
  0

• Exon is not exactly recognized

  #47 opened 5 years ago by KMgoo
  12

• An error during Filtering junctions

  #46 opened 5 years ago by KMgoo
  12

• Investigate use of cross validation for selecting cutoff values.

  #24 opened 5 years ago by maplesond
  1

• Adapt initial positive set to sequencing depth and read length

  #27 opened 7 years ago by maplesond
  1

• High Novel Splicce Junction Rate

  #44 opened 5 years ago by jgockley62
  6

• error in portcullis bamfilt

  #42 opened 5 years ago by wenbinmei
  13

• [BUG] make check fails with conda python

  #38 opened 6 years ago by lucventurini
  3

• Make portcullis work with long reads: ideas

  #41 opened 6 years ago by lucventurini
  12

• [BUG] Brew installation now broken after the release of Python 3.7

  #35 opened 7 years ago by lucventurini
  1

• Streamline boost subset

  #32 opened 6 years ago by maplesond
  1

• Parsing Command Line: too many positional options have been specified on the command line

  #37 opened 6 years ago by dfermin
  1

• how does portcullis handle antisense reads?

  #40 opened 6 years ago by mparker2
  1

• [Singularity] Installation fails, even following instructions in the recipe in the Repo

  #36 opened 6 years ago by lucventurini
  2

• conda conflicts with enum34?

  #34 opened 7 years ago by maximilianh
  2

• terminate called after throwing an instance of 'boost::exception_detail::clone_impl<portcullis::JunctionException>' what(): std::exception**

  #25 opened 7 years ago by fcamara7
  10

• Added sort / reindex and prefix options to junctools set

  #28 opened 7 years ago by maplesond
  0

• Ensure unique id after junctools set union

  #29 opened 7 years ago by maplesond
  0

• Speed up rule based filtering

  #26 opened 7 years ago by maplesond
  2

• Broken junctools convert due to changes in the tab format

  #31 opened 7 years ago by lucventurini
  2

• Counts of R1 and R2 for each strand

  #30 opened 7 years ago by maplesond
  1

• Configure with python3

  #21 opened 8 years ago by colindaven
  13

• Use score instead of coverage for the BED/GFF/GTF output

  #19 opened 8 years ago by lucventurini
  2

• Improve performance of rule-based filtering

  #23 opened 8 years ago by maplesond
  2

• Trouble starting with non-standard python3

  #22 opened 8 years ago by IanSudbery
  4

• Define primary junctions

  #20 opened 8 years ago by lucventurini
  0

• Portcullis filter dies if the output folder does not exist

  #16 opened 8 years ago by lucventurini
  2

• [0.16.0] Portcullis filter dies as it cannot find the junction file

  #18 opened 8 years ago by lucventurini
  5

• Personalise GFF source field in the output

  #17 opened 9 years ago by lucventurini
  1