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TobyBaril
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EarlGrey
Earl Grey: A fully automated TE curation and annotation pipeline
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Out of Memory but the job seemed already finished
#143
ting-hsuan-chen
opened
2 days ago
3
Revert "Patches for v4.4.6"
#142
TobyBaril
closed
4 days ago
0
Patches for v4.4.6
#141
TobyBaril
closed
4 days 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 week ago
2
Long running time
#139
sherlock0088
opened
1 week ago
2
Singularity container initial setup not working
#138
MikeSanJose
opened
1 week ago
4
sa-ssr: command not found
#137
r-mashoodh
opened
1 week ago
1
RepeatMasker complains about invalid species search term (but runs at Gitpod)
#136
trypchromics
opened
2 weeks ago
5
runtime in TEstrainer ultralong for *some* genomes
#135
estolle
opened
3 weeks ago
5
Warning: malformed fasta index file
#134
JonEilers
closed
1 week ago
3
unclassified TE
#133
PengfeiInTuebingen
closed
1 month ago
1
can not generate Repeat Landscapes showing TE activity
#132
skuri1222
closed
1 month ago
2
RepeatModeler always runs with 1 thread, does not reuse earlier round results
#131
mjacksonhill
closed
2 weeks ago
4
perl locale warning in Singularity container
#130
mjacksonhill
closed
1 month ago
2
Update soft masking option to avoid maskfasta bug
#129
DustinSokolowski
closed
2 months ago
0
Conda install error
#128
Glfrey
closed
2 weeks ago
6
Gff3 Question
#127
sherlock0088
closed
2 months ago
1
Only generating pie plot and no other summary plots
#126
johannabeam
closed
1 month ago
4
-recoverDir option for RepeatModeler?
#125
r-mashoodh
closed
2 months ago
2
Merge pull request #123 from TobyBaril/main
#124
TobyBaril
closed
2 months ago
0
reconciliation
#123
TobyBaril
closed
2 months ago
0
Calculation of LTR insertion time
#122
JMUwenjian
closed
2 months ago
2
[E::fai_read] Could not understand FASTA index and RepeatLandscape
#121
enriquepola1996
closed
2 months ago
7
ModuleNotFoundError at TEstrainer stage
#120
kiran-lee
closed
2 months ago
8
Summary plot fails because `bc` is missing (maybe)
#118
chriswyatt1
closed
1 month ago
5
Compared with repeatmodeler + repeatmasker, earlgrey annotated the bases masked of the transposon at a lower proportion
#117
wanjiujiu
closed
2 months ago
5
EG4.0.8 vs EG 4.2.4
#116
ekaralashvili
closed
2 months ago
3
overextension of TEs
#115
ferrojm
closed
3 months ago
2
Patches for Release 4.3.0
#114
TobyBaril
closed
3 months ago
0
Relaunching divergence calculation
#113
SwiftSeal
closed
3 months ago
5
RepeatMasker fails upon finishing
#112
DrPintoThe2nd
closed
2 months ago
5
annotations in gff file not shown in IGV
#111
ting-hsuan-chen
closed
3 months ago
3
Question about error
#110
mylena-s
closed
4 months ago
2
Installation Errors following "Earl Grey Installation and Configuration (If you already have RepeatMasker and RepeatModeler)"
#109
ufaroooq
closed
4 months ago
2
RepeatModeler run successfully, but did not create *.classified file and *-families.fa, and so stopped the earlGrey.
#108
jaehakson
closed
4 months ago
8
impact of initial ,masking by RM and usage of DFAM3.8
#107
estolle
closed
4 months ago
5
Patch v4.2.4
#106
TobyBaril
closed
4 months ago
0
data for pie chart proportions
#105
baligpanossian
closed
3 months ago
9
Stuck at the "Cleaning Genome" phase
#104
rpianezza
closed
4 months ago
7
102 bug when using soft link to genome
#103
TobyBaril
closed
4 months ago
0
Bug when using soft link to genome
#102
mylena-s
closed
4 months ago
1
Version 4.2.0 - Increased Efficiency and Patch Fixes
#101
TobyBaril
closed
5 months ago
0
Generate soft-masked genome without re-running?
#100
YingChen94
closed
5 months ago
2
GFF attributes and wrong TE classification??
#99
DhakadPankaj
closed
5 months ago
1
R step 12 "no"?
#98
YingChen94
closed
5 months ago
1
Variation in annotation within species/family
#97
lesserof2weevils
closed
4 months ago
2
Limiting Repeatmodeler rounds to 4/5 ??
#96
DhakadPankaj
closed
5 months ago
3
Filtering overlapping repeats for chimers
#95
pellescholten
closed
5 months ago
3
Error while using a custom library
#94
azotta
closed
5 months ago
2
Runtime and Restarting
#93
rpyron
closed
5 months ago
1
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