issues
search
NBISweden
/
AGAT
Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
GNU General Public License v3.0
477
stars
58
forks
source link
issues
Recently updated
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
add pe,sv,os from uniprot db header, evalue from blast output
#519
Juke34
closed
5 hours ago
0
# fix 516
#518
Juke34
closed
1 week ago
0
Fix #512
#515
Juke34
closed
1 week ago
1
`agat_sp_flag_short_introns.pl` not flagging a 1 bp intron
#516
GallVp
closed
1 week ago
5
installation failure due to missing perl module perl-clone
#511
abr5988
closed
1 week ago
1
agat_sp_filter_by_ORF_size.pl is not isoform aware
#512
GallVp
closed
1 week ago
7
GFF2GTF long_terminal_repeat being reported as transcript in gtf
#517
sivasubramanics
closed
4 weeks ago
1
Mismatched Protein Annotations Due to ID Format Inconsistencies Between BLAST and GFF3 Files
#513
joana-morais
opened
1 month ago
1
Fix typo in manual installation section of README.md
#514
dgruano
closed
1 month ago
1
445 bug version 1.3.2
#446
Juke34
closed
9 months ago
0
fix #507 - add option raw to print raw data in a dedidcated folder
#510
Juke34
closed
1 month ago
0
update doc
#490
Juke34
closed
4 months ago
0
Clean l1
#491
Juke34
closed
4 months ago
0
fix #457 remove attribute in gene_id and transcript_id to keep only the first …
#496
Juke34
closed
1 month ago
0
agat_sp_merge_annotations.pl output incompatible with cellranger
#457
LliliansCalvo
closed
1 month ago
40
AGAT compatible with Perl 5.36 ?
#392
eylenth
closed
1 month ago
10
agat_sp_statistics.pl for outputing whole distribution results as csv format
#507
Jasminefyh
closed
1 month ago
5
How to merge two genes with overlapping positions but no overlapping CDS?
#468
binzhengbin
opened
7 months ago
10
Fix issue with Perl>5.36
#509
Juke34
closed
1 month ago
1
AGAT not working in perl 5.38
#416
kgaisser
closed
1 month ago
7
perl 5.38 agat1.4 blankfile
#485
18700951101
closed
1 month ago
2
AGAT extracted only very small set of CDS from the *.gff3 and assembly file. Is there any probelm with the pipeline?
#501
Vijithkumar2020
closed
1 month ago
9
500K Gene Models with Many Short Sequences: Valid AGAT Output or Command Error?
#495
Vijithkumar2020
closed
1 month ago
1
Failed execution on Singularity
#500
jyw-atgithub
opened
3 months ago
1
Provide option for padding with agat_sp_manage_IDs.pl?
#508
dirkjanvw
closed
1 month ago
7
AGAT not working/not installed properly
#480
vaneet-lotay
closed
4 months ago
5
Fix #475 : Added an option to refer a folder of GFF files
#476
IvanUgrin
closed
4 months ago
2
EXCEPTION: Bio::Root::Exception
#506
bijendrabio
closed
2 months ago
2
Lines missing after using agat_convert_sp_gff2gtf.pl
#502
JC-therea
closed
3 months ago
6
agat_sp_flag_premature_stop_codons.pl mostly flags genes without premature stop codons
#504
JWDebler
opened
3 months ago
4
agat_sp_add_start_and_stop.pl MSG: Each line of the file must be less than 65,536 characters. Line 28 is 85016 chars.
#505
Xueliang24
closed
3 months ago
1
AGAT combine with high duplicated BUSCOs
#407
ld9866
closed
1 year ago
7
agat_convert_minimap2_bam2gff.pl handle Insertion and deletion
#503
tjwu
opened
3 months ago
0
AGAT installation - "make test " shows two failed tests.
#499
Vijithkumar2020
closed
3 months ago
5
Extraction of all transcripts from the AUGUSTUS output *.gff dat. Confused with the appropriate AGAT command.
#498
Vijithkumar2020
closed
3 months ago
2
use AGAT::AGAT
#497
antzellie
closed
3 months ago
7
500K Gene Models with Many Short Sequences: Valid AGAT Output or Command Error?
#494
Vijithkumar2020
closed
3 months ago
1
Error with GFF input file when using agat_sp_add_introns.pl and agat_convert_sp_gxf2gxf.pl
#493
mspopecki
opened
3 months ago
1
The agat_sp_filter_feature_by_attribute_value.pl installed by conda is an old version
#492
dongdongdong0203
opened
4 months ago
1
Split a gff3 file based on specified coordinates
#73
sanyalab
closed
3 years ago
2
Retain all isoforms, skip isoform duplicates from agat_sp_merge tool
#275
callumparr
closed
2 years ago
13
Support gezipped fasta/gtf/gff for agat_sp_extract_sequences.pl
#486
Tong-Chen
closed
4 months ago
1
agat_sp_extract_sequences.pl extract all CDS on gene level
#474
fuesseler
closed
4 months ago
2
Stat
#489
Juke34
closed
4 months ago
0
agat statistics enhancement request
#307
sanyalab
closed
4 months ago
2
fix #484
#488
Juke34
closed
4 months ago
0
No gene name when conversion from gff3 to gtf
#484
desmodus1984
closed
4 months ago
1
sort tag L2
#487
Juke34
closed
4 months ago
0
Mfannot - big improvement in handling this conversion
#483
Juke34
closed
4 months ago
0
Fix #471 - agat_sp_filter_feature_by_attribute_value.pl
#473
Juke34
closed
6 months ago
0
Next