gpertea gffread issues - Githubissues

gpertea / gffread

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more

MIT License

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issues

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output file only contains ENSEMBL gene ID and fasta sequence

#90 thibui1996 opened 2 years ago
1
From gtf to gff3

#89 marco91sol opened 2 years ago
0
Any way to keep the last stop codon results(*) when using -y option?

#88 xiekunwhy opened 2 years ago
1
Format issues between gffread versions

#87 EA2106-Universite-Francois-Rabelais opened 2 years ago
0
Gene range inferred wrongly for pseudo-autosomal genes

#86 hukai916 opened 2 years ago
0
Multiple Errors ---discarding overlapping duplicate gene feature

#85 Liyong-Zhang opened 2 years ago
2
handling for empty transcript_id

#84 murphyte closed 2 years ago
5
Speed up of gffread

#83 sanyalab closed 1 year ago
0
unexpected Ns added to transcripts fasta

#82 ramiroricardo opened 3 years ago
0
Conversion from BED input uses "BED" as feature name

#81 bernt-matthias opened 3 years ago
2
Allow locus attribute on table output

#80 ljyanesm opened 3 years ago
0
Unexpected output style when extracting fasta sequence from genome based on the gff file

#79 yjx1217 opened 3 years ago
0
shorter transcript not discarded using -K

#78 krabapple closed 3 years ago
8
Gffread extracts the wrong nucleotides from genome?

#77 stephanbitterwolf closed 3 years ago
1
Output issues for the -w, -x, and -y options

#76 sjfleck opened 3 years ago
2
cannot open input file (gff)

#75 Dongho1234 closed 3 years ago
0
GTF output file is different from GFF3 input file

#74 eduardopdev opened 3 years ago
7
Gzip support

#73 starskyzheng opened 3 years ago
1
Fix --version argument

#72 alephreish closed 3 years ago
1
-F does not write the features info

#71 husensofteng closed 3 years ago
9
Make -W (exon coordinates) argument work for -y (translations)

#70 alephreish closed 3 years ago
0
remove duplicated lines

#69 Maarten-vd-Sande closed 3 years ago
1
Include GTF "transcript_version" attribute in .fa transcript name

#68 ACastanza closed 3 years ago
10
gffread extracts wrong transcript sequence from reference FASTA

#67 LeonardoFurci closed 4 years ago
1
Extract intron seq

#66 bsb2014 opened 4 years ago
0
CDS phase: -H has no effect

#65 alephreish closed 3 years ago
1
empty files after running gffread with -x or -y

#64 JonEilers opened 4 years ago
2
gffread installation

#63 xiaolinchu92 closed 3 years ago
1
Option to avoid adding StopCodon when converting GTF to GFF

#62 estolle opened 4 years ago
0
Please send the version output to stdout and NOT stderr

#61 Gaura opened 4 years ago
0
build failure: GStrSet is not a template

#60 joelb123 closed 4 years ago
2
gffread does not seem to use the .fai files it creates.

#59 NDHall closed 4 years ago
3
Meaning of headline

#58 biozhangzhou opened 4 years ago
0
Incorrect gene line and gene coordinates with options --keep-genes -C

#57 gemygk opened 4 years ago
2
Segfault when --keep-genes is combined with -C

#56 mrvollger closed 4 years ago
1
Some genes lack 'exon' annotations after GFF3 to GTF conversion

#55 wflynny closed 4 years ago
2
GTF to GFF3: recover (or infer) gene feature

#54 LehmannN closed 4 years ago
7
citation for gffread

#53 fgypas closed 4 years ago
6
extract cds sequence +- given bases

#52 vivekbhr opened 4 years ago
1
Issue in reading CDS from GMAP-generated GFF3 file

#51 pckorhon opened 4 years ago
0
Extract cds/protein/exon sequence name show geneid

#50 liu-wq opened 4 years ago
4
Release v0.11.7 to CCB software download page

#49 jma1991 closed 4 years ago
2
conversion of gtf to fasta file?

#48 mathavanpu closed 4 years ago
3
CDS and protein sequences missing first base when exon line not present

#47 monicabritton opened 4 years ago
1
Cannot extract attributes when specifying the --table parameter

#46 jma1991 closed 4 years ago
2
missing gene id after converting gff to gtf

#45 ze236789 closed 4 years ago
2
getGenePositions issue

#44 birsandhu opened 4 years ago
0
--no-psuedo option does not seem to work

#43 lparsons closed 5 years ago
2
Gffread to extract transcript sequences from transcript assembly GTF file

#42 Aishah17 opened 5 years ago
2
GVF format

#41 rsalz opened 5 years ago
0

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