pmelsted/pizzly issues and pull requests

#46 - Pizzly with single-end data

Issue - State: open - Opened by andreyurch about 1 year ago

#46 - Pizzly with single-end data

Issue - State: open - Opened by andreyurch about 1 year ago

#45 - Max insert size from Kallisto

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

#45 - Max insert size from Kallisto

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

#44 - Segmentation Fault

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

#44 - Segmentation Fault

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

#43 - Provide a long option for `-k`

Pull Request - State: open - Opened by nh13 over 2 years ago

#43 - Provide a long option for `-k`

Pull Request - State: open - Opened by nh13 over 2 years ago

#42 - fusion locations

Issue - State: open - Opened by jlgabre almost 3 years ago

#42 - fusion locations

Issue - State: open - Opened by jlgabre almost 3 years ago

#41 - Because of dependence on Kallisto, is it necessary to trim?

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

#41 - Because of dependence on Kallisto, is it necessary to trim?

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

#40 - Bad Alloc error and no .hd5 file being generated

Issue - State: open - Opened by rahul-yadav-supra over 4 years ago

#40 - Bad Alloc error and no .hd5 file being generated

Issue - State: open - Opened by rahul-yadav-supra over 4 years ago

#39 - Working version of pizzly available?

Issue - State: open - Opened by mapostolides almost 5 years ago - 2 comments

#39 - Working version of pizzly available?

Issue - State: open - Opened by mapostolides almost 5 years ago - 2 comments

#38 - handling duplicated sequences in output.fusions.fasta

Issue - State: open - Opened by racng almost 5 years ago

#38 - handling duplicated sequences in output.fusions.fasta

Issue - State: open - Opened by racng almost 5 years ago

#37 - scripts/flatten_json.py - too unspecific to have in /usr/bin

Issue - State: open - Opened by smoe almost 5 years ago

#37 - scripts/flatten_json.py - too unspecific to have in /usr/bin

Issue - State: open - Opened by smoe almost 5 years ago

#36 - license of data files shipping in "test" folder?

Issue - State: open - Opened by smoe almost 5 years ago

#36 - license of data files shipping in "test" folder?

Issue - State: open - Opened by smoe almost 5 years ago

#35 - "seqan::ParseError" debugging

Issue - State: open - Opened by amwa about 5 years ago

#35 - "seqan::ParseError" debugging

Issue - State: open - Opened by amwa about 5 years ago

#34 - "pizzly: Not enough arguments were provided"

Issue - State: open - Opened by AmrR101 about 5 years ago - 1 comment

#34 - "pizzly: Not enough arguments were provided"

Issue - State: open - Opened by AmrR101 about 5 years ago - 1 comment

#33 - pizzly splitcount 0

Issue - State: open - Opened by igordot over 5 years ago - 1 comment

#33 - pizzly splitcount 0

Issue - State: open - Opened by igordot over 5 years ago - 1 comment

#32 - question on the confidence of the fusion gene transcripts

Issue - State: open - Opened by maximillo almost 6 years ago

#32 - question on the confidence of the fusion gene transcripts

Issue - State: open - Opened by maximillo almost 6 years ago

#31 - Long read RNA seq

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

#31 - Long read RNA seq

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

#30 - Unknown error when attempting to run pizzly

Issue - State: open - Opened by MichaelPisano over 6 years ago - 1 comment

#30 - Unknown error when attempting to run pizzly

Issue - State: open - Opened by MichaelPisano over 6 years ago - 1 comment

#29 - using pizzly on Augustus predictions

Issue - State: open - Opened by evolgenomology over 6 years ago

#29 - using pizzly on Augustus predictions

Issue - State: open - Opened by evolgenomology over 6 years ago

#28 - splitcount = 0

Issue - State: open - Opened by mathieu-massaviol over 6 years ago

#28 - splitcount = 0

Issue - State: open - Opened by mathieu-massaviol over 6 years ago

#27 - Long run time on very large RNAseq data

Issue - State: closed - Opened by chrisamiller over 6 years ago - 2 comments

#27 - Long run time on very large RNAseq data

Issue - State: closed - Opened by chrisamiller over 6 years ago - 2 comments

#26 - Segmentation fault: 11

Issue - State: open - Opened by ttamho over 6 years ago - 1 comment

#26 - Segmentation fault: 11

Issue - State: open - Opened by ttamho over 6 years ago - 1 comment

#25 - could not find any transcript sequences check that the ids in the FASTA file and GTF file match

Issue - State: closed - Opened by tuan-tt about 7 years ago

#25 - could not find any transcript sequences check that the ids in the FASTA file and GTF file match

Issue - State: closed - Opened by tuan-tt about 7 years ago

#24 - Extracting reads/read pairs mapping to fusions

Issue - State: open - Opened by virajbdeshpande about 7 years ago

#24 - Extracting reads/read pairs mapping to fusions

Issue - State: open - Opened by virajbdeshpande about 7 years ago

#23 - Running with more than one file for left/right reads

Issue - State: open - Opened by holtgrewe over 7 years ago - 1 comment

#22 - GTF file must be sorted in gene->transcript->exon order

Issue - State: open - Opened by roryk over 7 years ago

#21 - pizzly cache format

Issue - State: closed - Opened by roryk over 7 years ago - 1 comment

#20 - pep8 fixes

Pull Request - State: open - Opened by bgruening over 7 years ago - 1 comment

#19 - pizzly missing a fusion from SRR1659964

Issue - State: open - Opened by roryk over 7 years ago - 14 comments

#18 - Update README with gene collapsing and insert size commands.

Pull Request - State: open - Opened by roryk over 7 years ago - 4 comments

#17 - pizzly reports more fusions than expected

Issue - State: closed - Opened by roryk over 7 years ago - 1 comment

#16 - Error, could not find any transcript sequences

Issue - State: open - Opened by ndaniel over 7 years ago - 5 comments

#15 - Failed in installing pizzly

Issue - State: closed - Opened by qindan2008 over 7 years ago - 3 comments
Labels: bug

#14 - Change license and add Bioconda pkg

Pull Request - State: closed - Opened by bgruening over 7 years ago

#13 - Notes and compiled download don't match

Issue - State: open - Opened by lachlansimpson over 7 years ago - 1 comment
Labels: bug

#12 - Make Error; unable to compile required .c file

Issue - State: closed - Opened by sowmyaiyer over 7 years ago - 1 comment
Labels: bug

#11 - Non-printable characters (including ASCII 0) in fusion output FASTA sequences

Issue - State: closed - Opened by kreil over 7 years ago - 3 comments
Labels: bug

#10 - How does pizzly work ?

Issue - State: closed - Opened by ahy1221 over 7 years ago - 1 comment

#9 - Filtering criteria & downstream analysis

Issue - State: closed - Opened by leiendeckerlu over 7 years ago - 3 comments

#8 - segmentation fault

Issue - State: closed - Opened by kreil over 7 years ago - 22 comments

#7 - no fusion in output files

Issue - State: closed - Opened by doublehelixlf almost 8 years ago - 17 comments

#6 - update test/reads_*.fastq.gz such that .1 and .2 are removed from reads ids

Pull Request - State: open - Opened by ndaniel almost 8 years ago

#5 - Insert size estimate by Kallisto

Issue - State: closed - Opened by uros-sipetic almost 8 years ago - 4 comments

#4 - No fusion found

Issue - State: closed - Opened by bioinfo-dirty-jobs almost 8 years ago - 9 comments

#3 - Installation Problem

Issue - State: closed - Opened by bioinfo-dirty-jobs almost 8 years ago - 3 comments

#2 - False positive fusions and missed fusions

Issue - State: closed - Opened by ndaniel almost 8 years ago - 11 comments

#1 - --cache index.cache.txt

Issue - State: closed - Opened by ndaniel almost 8 years ago - 2 comments

GitHub / pmelsted/pizzly issues and pull requests