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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Not retrieving full transcripts from GFF3, only coding segments (this is without the -C parameter)

#140 vaneet-lotay opened 3 weeks ago
0
Error at GDynArray: cannot add item, maximum count reached!

#139 Fengyaa opened 4 weeks ago
0
the output gtf file coordinates is different from output fasta

#138 litun-fkby opened 1 month ago
0
conversion from .gff3 to .gtf results in empty .gtf file

#137 jsnoliva opened 2 months ago
1
issue with the suffix of tarnscripts ID

#136 yanyew closed 3 months ago
2
Unable to extract gene name

#135 kishor2019 opened 5 months ago
0
*** stack smashing detected ***: gffread terminated

#134 dengyang111 opened 7 months ago
4
What does the -r option do in gffread?

#133 zigge90 opened 8 months ago
1
Please delete my post

#132 santataRU opened 8 months ago
0
-E prints errors but cannot find a way to write errors to a file

#131 Angsty-Wondergirl opened 8 months ago
0
The option "-S" does not work

#130 sanyalab opened 9 months ago
0
gffread -w works but not -x and -y

#129 Ruiqi-CUB opened 10 months ago
2
Segmentation fault --- exact cds and protein from genome

#128 710744562 opened 10 months ago
0
CDS and protein

#127 Gon1976 opened 11 months ago
0
Enhancement request: Smaller Gff3 from a larger file

#126 sanyalab opened 1 year ago
0
Large genome or large chromosome

#125 xiekunwhy opened 1 year ago
4
install error

#124 mick42-star closed 7 months ago
3
How does --sort-by work?

#123 juanjo255 closed 3 months ago
0
Wrong thread, could you please delete the issue.

#122 artemyzhigulev opened 1 year ago
0
double free or corruption (!prev) and gff corruption with ribosomal slippage

#121 alephreish opened 1 year ago
1
converted gtf file is empty

#120 sumitra20 opened 1 year ago
1
bad error message when command line option mistyped

#119 diekhans opened 1 year ago
0
The converted gtf file sizes 0 bytes

#118 183136 opened 1 year ago
1
about get transcript.fa from gtf file

#117 siyuyang1013 opened 1 year ago
0
Warning: couldn't find fasta record for 'LG03'

#116 Alalakikun closed 1 year ago
2
gffread to protein

#115 bijendrabio opened 1 year ago
3
Missing gene_id for trans-splicing exons when converting gff to gtf

#114 Fan-iX opened 1 year ago
0
problem with stopcodons in-frame encoding selenocysteine

#113 MiSchwabe opened 1 year ago
0
CDS gets filtered out and its attributes overwrite attributes for another CDS in the same gene

#112 hermidalc opened 2 years ago
2
pseudo feature not filtered with `--no-pseudo` and `-F` options together

#111 hermidalc opened 2 years ago
0
Failure to convert gene and child CDSes to exons with parent mRNAs which are children of gene

#110 hermidalc opened 2 years ago
0
Incorrect change of intron to mRNA feature

#109 hermidalc opened 2 years ago
0
Segmentation fault or corrupted output GFF when using `-C` coding only option on multiple NCBI genome assembly GFF files

#108 hermidalc opened 2 years ago
1
Error parsing strand (?) from GFF line

#107 hermidalc opened 2 years ago
2
The ID attribute of CDS and exon features in the output gff3 is missing

#106 tiramisutes opened 2 years ago
1
Keep gene ID

#105 xiekunwhy closed 2 years ago
1
-H still has no effect on the output gff

#104 krabapple opened 2 years ago
0
--add-hasCDS not a recognized argument

#103 krabapple opened 2 years ago
0
Output proteome file has unexpected sequences

#102 alexvasilikop closed 1 year ago
2
Error in `gffread': double free or corruption (!prev): 0x000055b181794a50 ***

#101 Biscuite-wzy opened 2 years ago
0
empty output of cds.fa

#100 Liyong-Zhang opened 2 years ago
1
Problem of overflow

#99 thecgs opened 2 years ago
0
gffread recognizes and converts

#98 choiseungji opened 2 years ago
0
option --nc not supported

#97 tbazilegith closed 2 years ago
5
Installation Failure

#96 Botantisty opened 2 years ago
2
Suggestion to support syntax for bcftools csq

#95 lindenb opened 2 years ago
0
Error: no genomic sequence available (check -g option!).

#94 raita27 closed 2 years ago
5
make the defline of FASTA output more consistent

#93 gpertea opened 2 years ago
0
Pathological CDS annotation classified as having no issues due to phase handling

#92 nicolasrochette opened 2 years ago
0
GffObj::getSpliced() error: improper

#91 abcdefghijklmn97 opened 2 years ago
2