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oushujun
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LTR_retriever
LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/
GNU General Public License v3.0
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What is the difference between LTR Unknown and NA Unknown?
#123
jia-wu-feng
closed
2 years ago
5
Too many 0 LAI values
#122
Wenwen012345
closed
2 years ago
1
RepeatMasker is not running properly
#121
qingyun-mei
closed
1 year ago
13
GFFCompare
#120
Wenwen012345
closed
2 years ago
2
Stoped in the annotation step
#119
Wenwen012345
closed
2 years ago
4
perl call_seq_by_list.pl is not working
#118
Ravindra-Raut
closed
1 year ago
8
About ltr_harvest output
#117
cherrie-g
closed
1 year ago
2
LAI seems not working...
#116
xiahouzuoying
closed
2 years ago
7
Cannot complete in-place edit
#115
Wenwen012345
closed
2 years ago
2
should we only keep the pseudochromosome for caculating the LAI?
#114
wbglizhizhong
closed
2 years ago
2
What's the rationale of having IDs shorter than 15 bits?
#113
BioFalcon
closed
2 years ago
1
BLASTN replaced by BLAT
#112
cherrie-g
closed
2 years ago
3
Fix undercounting of solo and intact elements in solo_intact_ratio.pl
#111
eernst
closed
1 year ago
0
A bug in solo_intact_ratio.pl
#110
xie-wei-hh
closed
1 year ago
5
LTR_retriever has been running for more than 48 hours without results
#109
yangfty
closed
2 years ago
2
Could LTR_retriever give the annotation of the components of TE?
#108
ttbond
closed
2 years ago
2
Issue with bin/make_lib.pl
#107
RanZhou
closed
2 years ago
3
xxx.genome.defalse is empty and the soft seems aborted
#106
zouxq97
closed
2 years ago
4
can't find find_ltr_dawgPaws.pl
#105
gfanglei
closed
2 years ago
1
cp: cannot stat ‘./sample.ssrmasked.fasta.retriever.scn.adj’: No such file or directory
#104
Biscuite-wzy
closed
2 years ago
17
Any possibility to use output of repeatmodeler for LAI evaluation?
#103
ghost
closed
2 years ago
1
main::main::postProcessSearch: FastaDB::substr - Error index out of bounds!
#102
Biscuite-wzy
closed
2 years ago
3
The calculate model for LTR-insertion time
#101
leeun67
closed
2 years ago
1
Solved: Can't exec "-misschar"
#100
timkahlke
closed
2 years ago
1
questions about solo LTR
#99
xiaoyezao
closed
2 years ago
5
How to judge the 5' and 3' LTR?
#98
liufuyan2016
closed
3 years ago
1
Suggestions for optimization
#97
andreaswallberg
closed
1 year ago
3
truncted LTR
#96
xiaoyezao
closed
3 years ago
3
LTR_FINDER_parallel and salvage mode
#95
anandksrao
closed
3 years ago
1
Reg. Copia, Gypsy, and Unknown or total LTR density calculation
#94
Yedomon
closed
3 years ago
12
sequence ID length limit constraint
#93
anandksrao
closed
3 years ago
1
Dependency checking: The RMblast engine is not installed in RepeatMasker
#92
Prabhu89-code
closed
3 years ago
8
Can't exec "-misschar"
#91
xiaoyezao
closed
3 years ago
2
Problems to install LTR_retriever
#90
rosaliapaz
closed
3 years ago
9
source for database files
#89
sarjopp
closed
3 years ago
2
DIRS-LTR and insert length question
#88
AlexdeMendoza
closed
3 years ago
2
LAI does not improve despite sequencing and assembly improvements
#87
oushujun
opened
3 years ago
21
Meaning of *.defalse file
#86
Weihankk
closed
3 years ago
7
assessing the performance of LTR_retriever
#85
sadikmu
closed
3 years ago
1
Can't exec "-misschar"
#84
Qiuming1986
closed
3 years ago
5
LAI for ployploid
#83
Jiny000
closed
3 years ago
4
LTR insertion time
#82
liulu0827
closed
3 years ago
7
File *nmtf.LTRlib.fa not made
#81
lcoombe
closed
3 years ago
11
Can i use "-noanno" options to accelerate the whole process?
#80
AntetokounmJie
closed
3 years ago
2
Calculate LTR insertion time using all LTR rather than only intact LTR
#79
xiaoyezao
closed
3 years ago
3
Something wrong with "-misschar"
#78
AntetokounmJie
closed
3 years ago
3
Added the dockerfile, might be useful for others
#77
aseetharam
closed
3 years ago
0
Error: cp: cannot stat *.retriever.scn.adj’: No such file or directory
#76
GrandH2O
closed
3 years ago
3
Help with interpretation of the output (.out.gff)
#75
ValentinaBoP
closed
4 years ago
2
Identify novel LTR sequences
#74
virginiascarlett
closed
4 years ago
1
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