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NBISweden
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AGAT
Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
GNU General Public License v3.0
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AGAT cannot access features_level1.json file (wrong shared folder location detected by File::Share)
#4
wuxiaopei0509
closed
2 years ago
47
agat_sp_merge_annotations.pl output incompatible with cellranger
#457
LliliansCalvo
closed
4 days ago
40
agat_convert_sp_gff2gtf.pl output empty file
#63
olechnwin
closed
4 years ago
28
agat_sp_manage_functional_annotation gene names
#192
ctxchris
closed
3 years ago
20
agat_sp_load_function_from_protein_align.pl - works only for Exonerate via MAKER.
#158
sarjopp
closed
1 year ago
20
Getting sensitivity and specificity scores at the mRNA level
#190
sanyalab
closed
3 years ago
18
agat_sp_extract_sequences.pl created empty files
#154
mictadlo
closed
3 years ago
17
Error converting RepeatMasker output file / New feature request
#102
githubgig
closed
3 years ago
17
Can't call method "strand" on an undefined value
#47
ChemaMD
closed
3 years ago
16
Issue agat_convert_minimap2_bam2gff.pl
#363
EglantineMB
closed
1 year ago
15
Conda install
#342
ndeimler99
closed
1 year ago
15
Can't locate Sort/Naturally.pm in @INC while running agat_convert_sp_gff2bed.pl
#231
Rohit-Satyam
closed
2 years ago
15
AGAT stopped at OmniscientI stage
#278
ardy20
closed
1 year ago
14
problems about the agat_sp_fix_fusion.pl
#228
Huangyizhong
closed
2 years ago
14
overlaps between subfeatures in the underlying annotation
#188
mictadlo
closed
2 years ago
14
features with more than one parent
#126
eduardopdev
closed
2 years ago
14
MSG: Each line of the fasta entry must be the same length except the last. Line above #3 '
#90
sstwins21
closed
3 years ago
14
agat_sp_keep_longest_isoform.pl can't open gff file
#31
b524198065
closed
4 years ago
14
Retain all isoforms, skip isoform duplicates from agat_sp_merge tool
#275
callumparr
closed
2 years ago
13
agat_sp_compare_two_annotations.pl and agat_sp_complement_annotations.pl
#289
EthanKhew
closed
1 year ago
12
agat_sp_extract_sequences.pl produces lots of warnings
#53
soungalo
closed
1 year ago
12
agat_sp_fix_longest_ORF.pl default codon table
#420
jvolkening
closed
5 months ago
11
Unable to convert GFF to GFT
#419
MrLocuace
closed
9 months ago
11
How to merge two genes with overlapping positions but no overlapping CDS?
#468
binzhengbin
opened
5 months ago
10
Converting .gff to .gtf for CellRanger
#434
matejasoretic
closed
9 months ago
10
AGAT compatible with Perl 5.36 ?
#392
eylenth
closed
1 week ago
10
gff3 reader warning: primary_tag error @ expressed_sequence_match still not taken into account! Please modify the json files to define the feature in one of the levels.
#283
Olivier144
closed
2 years ago
10
Issue in finding required dependencies
#48
timregan
closed
4 years ago
10
New script - add attributes from csv/tsv
#44
Juke34
closed
4 years ago
10
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 week ago
9
GTF→GFF3 conversion: Overlapping features with the same gene_id not recognized as the same gene
#207
jasonleongbio
closed
3 years ago
9
extract gene name and description from gff
#181
LeonardosMageiros
closed
3 years ago
9
strand directions are changed using agat_convert_bed2gff.pl
#135
herlianal12
closed
3 years ago
9
product not catched when GN missing in the header
#108
Juke34
closed
3 years ago
9
Feature request: To extract the TSS information from GTF file
#89
Rohit-Satyam
closed
3 years ago
9
Missing premature stop codons
#80
Neato-Nick
closed
4 years ago
9
agat_sp_extract_sequences.pl produced a shorter AA sequence
#20
mictadlo
closed
4 years ago
9
Problem with GFF to GTF conversion
#417
PavelKiryanov
closed
9 months ago
8
Bad end parameter.
#327
fangbohao
closed
1 year ago
8
strange gff causing gene number to double
#290
sjfleck
closed
1 year ago
8
Fixing gene and transcript missing features from tsebra.gtf for AGAT
#288
romseg
closed
2 years ago
8
container problem - cannot open file
#256
shhayat
closed
2 years ago
8
Help file
#255
PacoZm
closed
2 years ago
8
Flip gff3 annotations to match flipped sequences
#248
oushujun
closed
2 years ago
8
Can't call method "primary_tag" on an undefined value at /usr/local/bin/agat_convert_sp_gff2gtf.pl line 538.
#245
cihanerkut
closed
2 years ago
8
merging gff3 files when one is only cds
#221
jaredbernard
closed
2 years ago
8
Short Introns flagged with <pseudo> not accepted by ENA anymore
#151
schellt
closed
2 years ago
8
agat_convert_sp_gxf2gxf --gvi 2.5 not working
#60
JWDebler
closed
4 years ago
8
agat_sp_manage_functional_annotation.pl stuck for very long time computing statics
#43
mostafaabuzaid25
closed
4 years ago
8
Failed test: 31
#33
Tdanis
closed
4 years ago
8
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