Ecosyste.ms: Issues

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GitHub / gpertea/gffcompare issues and pull requests

#99 - 1. How to cluster transcripts from multiple query gtf files? 2. Something wired about tss_id

Issue - State: open - Opened by dudududu12138 26 days ago - 1 comment
Labels: to investigate

#98 - Filtering the gffcompare output files based on the class codes

Issue - State: closed - Opened by Anees-caas about 1 month ago - 1 comment

#97 - please tag a release.

Issue - State: open - Opened by EricDeveaud 2 months ago

#93 - GFFCompare ".tracking" file has zero value in<FPKM>|<TPM>|<cov> columns

Issue - State: closed - Opened by Miracle-Yao 5 months ago - 2 comments

#92 - Stringent comparison of CDS using --strict-match

Issue - State: open - Opened by etvedte 6 months ago

#91 - --cds-match to force matching CDS in addition to exon.

Pull Request - State: closed - Opened by alevar 7 months ago

#90 - No Sensitivity/Accuracy in the .stats output file

Issue - State: closed - Opened by YIGUIz 7 months ago

#89 - Should I filter the transcript with class code "s"?

Issue - State: open - Opened by JD12138 7 months ago - 1 comment

#88 - missing stringTie ID in gffcomapre tmap file

Issue - State: open - Opened by Vermarashi 10 months ago - 1 comment

#84 - Number of loci and mRNAs in reference keeps changing

Issue - State: closed - Opened by gbdias about 1 year ago - 1 comment

#82 - all input transcript attributes and features should be preserved in annotation mode

Issue - State: open - Opened by gpertea over 1 year ago
Labels: enhancement

#80 - A question on gffcompare

Issue - State: closed - Opened by sanyalab over 1 year ago

#79 - add option to assemble transfrags in the combined.gtf output

Issue - State: open - Opened by gpertea over 1 year ago - 1 comment
Labels: feature request

#78 - There is no CDS information in the generated file！

Issue - State: open - Opened by XK4959 almost 2 years ago

#77 - How is class code X is identified in stranded data?

Issue - State: open - Opened by srisarya about 2 years ago

#76 - Merging different gtf files

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

#75 - class_code 'u' in all transcripts

Issue - State: open - Opened by karlaarz over 2 years ago - 1 comment

#74 - Transcript classification codes ?

Issue - State: closed - Opened by hmyh1202 over 2 years ago - 1 comment

#73 - How to keep the CDS info for each transcript?

Issue - State: open - Opened by zmz1988 almost 3 years ago - 2 comments
Labels: enhancement

#71 - Extract transposon

Issue - State: open - Opened by Wenwen012345 almost 3 years ago - 1 comment

#70 - gff file and the XLOC numbers are not ordered correctly

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

#69 - Availability of new version on Conda and biocontainers

Issue - State: open - Opened by bayraktar1 almost 3 years ago

#68 - Definition of "Locus Level"

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

#67 - Comparing two different mouse strain gtf files

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

#66 - Where can I get gffcompare v0.12.5?

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

#65 - keep reference transcripts

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

#64 - Number of samples reported exceeds the maximum

Issue - State: closed - Opened by Akazhiel about 4 years ago - 3 comments
Labels: bug

#63 - gffcompare -d option not having effect

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

#62 - disable discard duplicate

Issue - State: open - Opened by BeatrizdeToledo over 4 years ago - 1 comment

#60 - How is 'tss_id' assigned?

Issue - State: open - Opened by junghoon-shin over 4 years ago

#57 - make: *** [Makefile:61: ../gclib] Error 127

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

#57 - make: *** [Makefile:61: ../gclib] Error 127

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

#56 - make: *** [gffcompare.o] Error 1

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

#55 - Lost reference mRNA during multiple assembly comparison

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

#54 - Intron chain level sensitivity is greater than 100%

Issue - State: closed - Opened by junghoon-shin over 4 years ago - 11 comments

#54 - Intron chain level sensitivity is greater than 100%

Issue - State: closed - Opened by junghoon-shin over 4 years ago - 11 comments

#52 - 0 reference transcripts loaded.

Issue - State: closed - Opened by nattzy94 over 4 years ago - 3 comments

#51 - switched to gene_id instead of gene_name in getGeneID by default

Pull Request - State: closed - Opened by alevar over 4 years ago - 2 comments

#50 - why -x and -y option print empty file

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

#49 - fixed the double tab in the tmap header line

Pull Request - State: closed - Opened by alevar over 4 years ago - 1 comment

#48 - Question on gffcompare output

Issue - State: closed - Opened by ljw90607 about 5 years ago - 10 comments

#47 - gffcompare shown wrong result when using strict-match

Issue - State: open - Opened by grassking100 about 5 years ago - 1 comment
Labels: bug

#46 - Why not two '='

Issue - State: open - Opened by wangshun1121 about 5 years ago - 1 comment

#45 - no refmap/tmap generated from gffcompare?

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

#44 - Exons and introns coordinates

Issue - State: open - Opened by fgypas about 5 years ago - 2 comments

#43 - Missing tmap and refmap files

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

#42 - Question: How do you find novel transcripts using GFFcompare?

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

#41 - how to unnderstand the *.stats file?

Issue - State: open - Opened by cuiuc12 over 5 years ago

#39 - question about code "="

Issue - State: open - Opened by lufeng891109 over 5 years ago - 1 comment

#38 - Fuzz matching of intron chains and exons

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

#37 - Error building gffcompare

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

#36 - too many input files (limit set to 500 at compile time)

Issue - State: open - Opened by ZhuangZK over 5 years ago - 4 comments

#35 - Sensitivity/Precision Stats

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

#34 - How can I extract the novel exons?

Issue - State: closed - Opened by ashokpatowary almost 6 years ago - 2 comments

#33 - Build fails

Issue - State: closed - Opened by trecakov almost 6 years ago - 4 comments

#32 - single-exon transcript in reference

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

#31 - Warning: reference transcript has undetermined strand, discarded.

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

#30 - Tagged Versions?

Issue - State: open - Opened by jrdemasi over 6 years ago - 3 comments

#29 - Memory corruption while running gffcompare

Issue - State: closed - Opened by Florianus almost 7 years ago - 4 comments

#28 - No coverage in .tmap file

Issue - State: open - Opened by zoewardnz almost 7 years ago - 1 comment

#27 - What's the mean of class code 'k'

Issue - State: closed - Opened by Trandamere almost 7 years ago - 5 comments

#26 - Class code 'NA' when it should be '='?

Issue - State: closed - Opened by zoewardnz almost 7 years ago - 5 comments
Labels: bug

#25 - gffcompare giving 'NA's

Issue - State: closed - Opened by zoewardnz almost 7 years ago

#24 - how to find novel genes and transcripts in gffcompare?

Issue - State: closed - Opened by naveenkumarv40 about 7 years ago - 2 comments

#22 - gffcompare class code "x", what is the minimum overlap?

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

#21 - gffcompare run on stringtie --merge gtf file results in zeros in the summary text

Issue - State: closed - Opened by adeslatt over 7 years ago - 2 comments

#19 - gffcompare fails to match gtf without chr prepended to chromosome names

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

#18 - Difficulty matching behavior between older and newer gffcompare

Issue - State: closed - Opened by bioinfomagician over 7 years ago - 6 comments
Labels: bug

#17 - Re: Deleted

Issue - State: closed - Opened by jfb4497 over 7 years ago

#16 - Error running gffcompare

Issue - State: open - Opened by lakhujanivijay almost 8 years ago - 3 comments

#15 - update release tags

Issue - State: closed - Opened by 0xaf1f almost 8 years ago - 1 comment

#14 - How to compare CDS gff with genome guided assembled gff

Issue - State: open - Opened by bioinfonext almost 8 years ago

#13 - definition for single-exon transcript

Issue - State: closed - Opened by shaomingfu almost 8 years ago - 1 comment

#11 - How to interpret sensitivity and precision?

Issue - State: closed - Opened by Vivianstats almost 8 years ago - 3 comments

#10 - How to statistics the novel transcripts

Issue - State: closed - Opened by Trandamere about 8 years ago - 2 comments

#9 - Only 1 output file, input GTF is overwritten (v0.9.9)

Issue - State: closed - Opened by malloryfreeberg about 8 years ago - 6 comments

#8 - Output path of refmap and tmap

Issue - State: closed - Opened by culpinnis about 8 years ago - 1 comment

#7 - Interpreting sensitivity and precision

Issue - State: closed - Opened by jstrohm about 8 years ago - 3 comments

#6 - gff compare gives identical results for multiple files

Issue - State: closed - Opened by jstrohm about 8 years ago - 3 comments

#5 - Error allocating memory

Issue - State: closed - Opened by ggirelli over 8 years ago - 5 comments

#4 - -G option no longer exists

Issue - State: closed - Opened by Jeltje over 8 years ago - 3 comments
Labels: question

#3 - cannot locate input file: –r [likely solution]

Issue - State: open - Opened by bassanio over 8 years ago - 7 comments