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TobyBaril
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EarlGrey
Earl Grey: A fully automated TE curation and annotation pipeline
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read only file system for fasta, and mkdir errors - with fix
#157
colindaven
closed
1 day ago
2
TE Strainer script issue
#156
saramiller23
opened
1 week ago
1
Soft-masking results from Earl Grey for Braker2 annotation
#155
lyy005
opened
1 week ago
2
File families.fa.strained is empty in the summaryFiles directory
#154
Zhenlisme
closed
2 weeks ago
4
Question about TEMP files
#153
jeankeller
closed
21 hours ago
2
Pipeline dies at building database
#152
kguynes
closed
2 weeks ago
3
Inquiry About Position Markings in GFF File
#151
chenyu26sohucom
closed
2 weeks ago
2
Updates for Version 5!
#150
TobyBaril
closed
1 month ago
0
Running EarlGrey with already available RepeatModeler Consensus file
#149
Homap
closed
1 month ago
3
Merged the output of earlgreylibconstruct
#148
sherlock0088
closed
1 month ago
1
Question: PanTE analyses for EarlGrey
#147
Chenglin20170390
closed
1 month ago
1
Add updates to README
#146
TobyBaril
closed
1 month ago
0
Resume from in-progress TEStrainer iterations
#145
mjacksonhill
opened
1 month ago
2
The progress appears quite slow for large genome
#144
joweihsieh
closed
1 month ago
1
Out of Memory but the job seemed already finished
#143
ting-hsuan-chen
opened
1 month ago
12
Revert "Patches for v4.4.6"
#142
TobyBaril
closed
1 month ago
0
Patches for v4.4.6
#141
TobyBaril
closed
1 month ago
0
RepeatModeler or RepeatMasker failed with EarlGrey v4.4.0 and RepeatMasker v4.15, lanscape.pdf missed and an extended runtime of RepeatModeler round with EarlGrey v4.4.0 and RepeatMasker v4.15
#140
manwensu
opened
1 month ago
4
Long running time
#139
sherlock0088
closed
1 month ago
3
Singularity container initial setup not working
#138
MikeSanJose
closed
1 month ago
11
sa-ssr: command not found
#137
r-mashoodh
closed
1 month ago
2
RepeatMasker complains about invalid species search term (but runs at Gitpod)
#136
trypchromics
opened
2 months ago
6
runtime in TEstrainer ultralong for *some* genomes
#135
estolle
opened
2 months ago
6
Warning: malformed fasta index file
#134
JonEilers
closed
1 month ago
3
unclassified TE
#133
PengfeiInTuebingen
closed
2 months ago
1
can not generate Repeat Landscapes showing TE activity
#132
skuri1222
closed
2 months ago
2
RepeatModeler always runs with 1 thread, does not reuse earlier round results
#131
mjacksonhill
closed
2 months ago
4
perl locale warning in Singularity container
#130
mjacksonhill
closed
2 months ago
2
Update soft masking option to avoid maskfasta bug
#129
DustinSokolowski
closed
3 months ago
0
Conda install error
#128
Glfrey
closed
2 months ago
6
Gff3 Question
#127
sherlock0088
closed
3 months ago
1
Only generating pie plot and no other summary plots
#126
johannabeam
closed
2 months ago
4
-recoverDir option for RepeatModeler?
#125
r-mashoodh
closed
4 months ago
2
Merge pull request #123 from TobyBaril/main
#124
TobyBaril
closed
4 months ago
0
reconciliation
#123
TobyBaril
closed
4 months ago
0
Calculation of LTR insertion time
#122
JMUwenjian
closed
4 months ago
2
[E::fai_read] Could not understand FASTA index and RepeatLandscape
#121
enriquepola1996
closed
4 months ago
7
ModuleNotFoundError at TEstrainer stage
#120
kiran-lee
closed
3 months ago
8
Summary plot fails because `bc` is missing (maybe)
#118
chriswyatt1
closed
2 months ago
5
Compared with repeatmodeler + repeatmasker, earlgrey annotated the bases masked of the transposon at a lower proportion
#117
wanjiujiu
closed
4 months ago
5
EG4.0.8 vs EG 4.2.4
#116
ekaralashvili
closed
4 months ago
3
overextension of TEs
#115
ferrojm
closed
4 months ago
2
Patches for Release 4.3.0
#114
TobyBaril
closed
5 months ago
0
Relaunching divergence calculation
#113
SwiftSeal
closed
5 months ago
5
RepeatMasker fails upon finishing
#112
DrPintoThe2nd
closed
4 months ago
5
annotations in gff file not shown in IGV
#111
ting-hsuan-chen
closed
5 months ago
3
Question about error
#110
mylena-s
closed
5 months ago
2
Installation Errors following "Earl Grey Installation and Configuration (If you already have RepeatMasker and RepeatModeler)"
#109
ufaroooq
closed
5 months ago
2
RepeatModeler run successfully, but did not create *.classified file and *-families.fa, and so stopped the earlGrey.
#108
jaehakson
closed
5 months ago
8
impact of initial ,masking by RM and usage of DFAM3.8
#107
estolle
closed
5 months ago
5
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