gpertea gffcompare issues

gpertea / gffcompare

classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF

MIT License

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issues

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

#91 alevar closed 2 weeks ago
0
No Sensitivity/Accuracy in the .stats output file

#90 YIGUIz closed 3 weeks ago
0
Should I filter the transcript with class code "s"?

#89 JD12138 opened 1 month ago
0
missing stringTie ID in gffcomapre tmap file

#88 rvermamsm opened 4 months ago
0
How can one visualize GFF files coverage, FPKM ; TPM values in a genome browser?

#87 pbuendia opened 5 months ago
0
"Warning: merging adjacent/overlapping segments" when using GFFCompare

#86 RobAlbn opened 6 months ago
0
GFFCompare ".tracking" file not containing all transcript IDs of all the provided annotation files

#85 RobAlbn opened 6 months ago
0
Number of loci and mRNAs in reference keeps changing

#84 gbdias closed 7 months ago
1
No sensitivity or precision stats reported if multiple gffs given as input

#83 gbdias opened 7 months ago
0
all input transcript attributes and features should be preserved in annotation mode

#82 gpertea opened 9 months ago
0
-p should rename transcripts even when running in "annotation mode" (single input file, no merge options)

#81 gpertea closed 6 months ago
0
A question on gffcompare

#80 sanyalab closed 3 weeks ago
0
add option to assemble transfrags in the combined.gtf output

#79 gpertea opened 1 year ago
1
There is no CDS information in the generated file！

#78 XK4959 opened 1 year ago
0
How is class code X is identified in stranded data?

#77 srisarya opened 1 year ago
0
Merging different gtf files

#76 TluckDucky opened 1 year ago
0
class_code 'u' in all transcripts

#75 karlaarz opened 1 year ago
1
Transcript classification codes ?

#74 hmyh1202 closed 2 years ago
1
How to keep the CDS info for each transcript?

#73 zmz1988 opened 2 years ago
2
Missing tmap and refmap files in query gff directory + missing statistics in stats file

#72 jchang97 opened 2 years ago
0
Extract transposon

#71 Wenwen012345 opened 2 years ago
1
gff file and the XLOC numbers are not ordered correctly

#70 dosshra opened 2 years ago
0
Availability of new version on Conda and biocontainers

#69 bayraktar1 opened 2 years ago
0
Definition of "Locus Level"

#68 gallardo-seq closed 2 years ago
2
Comparing two different mouse strain gtf files

#67 RNAseqer opened 2 years ago
0
Where can I get gffcompare v0.12.5?

#66 junghoon-shin closed 3 years ago
1
keep reference transcripts

#65 QiliShi opened 3 years ago
0
Number of samples reported exceeds the maximum

#64 Akazhiel closed 2 years ago
3
gffcompare -d option not having effect

#63 Akazhiel closed 3 years ago
1
disable discard duplicate

#62 BeatrizdeToledo opened 3 years ago
1
Exon-level sensitivity is not 100%, but there are zero missed exons.

#61 junghoon-shin opened 3 years ago
0
How is 'tss_id' assigned?

#60 junghoon-shin opened 3 years ago
0
replace '.' class code in .tracking and combined files with a concatenation of participant codes

#59 gpertea opened 3 years ago
0
.tracking file does not always show the 'closest' reference transcript for SETs

#58 junghoon-shin closed 3 years ago
4
make: *** [Makefile:61: ../gclib] Error 127

#57 yejilee-biostat closed 3 years ago
2
make: *** [gffcompare.o] Error 1

#56 TommySchooner closed 3 years ago
2
Lost reference mRNA during multiple assembly comparison

#55 CIWa closed 3 years ago
5
Intron chain level sensitivity is greater than 100%

#54 junghoon-shin closed 3 years ago
11
how to deal with falsely merged gene regions into one super-locus?

#53 Ruth-hals opened 4 years ago
0
0 reference transcripts loaded.

#52 nattzy94 closed 3 years ago
3
switched to gene_id instead of gene_name in getGeneID by default

#51 alevar closed 4 years ago
2
why -x and -y option print empty file

#50 fjptwenger closed 4 years ago
1
fixed the double tab in the tmap header line

#49 alevar closed 4 years ago
1
Question on gffcompare output

#48 ljw90607 closed 3 years ago
10
gffcompare shown wrong result when using strict-match

#47 grassking100 opened 4 years ago
1
Why not two '='

#46 wangshun1121 opened 4 years ago
1
no refmap/tmap generated from gffcompare?

#45 yejilee-biostat closed 4 years ago
3
Exons and introns coordinates

#44 fgypas opened 4 years ago
2
Missing tmap and refmap files

#43 fgypas closed 4 years ago
2
Question: How do you find novel transcripts using GFFcompare?

#42 chahatupreti opened 5 years ago
1