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sestaton
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tephra
A tool for discovering transposable elements and describing patterns of genome evolution
MIT License
30
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Question about how to run Tephra correctly?
#51
CSU-KangHu
opened
11 months ago
6
Report bugs
#50
naishikawa
opened
2 years ago
3
Make test errors
#49
pasviber
closed
2 years ago
9
issue with gene file
#48
jcerca
opened
3 years ago
3
Problem with install
#47
bioinformaticaInta
opened
4 years ago
2
sh: 0: Illegal option -j
#46
jguhlin
opened
4 years ago
5
Report a bug
#45
altingia
closed
4 years ago
2
singularity container doesn't contain perldoc
#44
nhartwic
closed
4 years ago
2
Singularity yml parsing error
#43
eganko
opened
4 years ago
15
problem running findtirs
#42
JennyHTLee
opened
5 years ago
5
Configure all external programs, even if they exist in PATH
#41
sestaton
closed
5 years ago
0
Install via singularity
#40
oushujun
opened
5 years ago
7
Makefile.PL error
#39
dejonggr
opened
5 years ago
9
Error running tephra age command
#38
davidecarlson
closed
4 years ago
6
Error Makefile.PL
#37
ohan-Bioinfo
opened
5 years ago
8
LTR Age output
#36
DiegoZavallo
opened
5 years ago
8
ages file has different LTR names
#35
juancresc
opened
5 years ago
4
Can we run the command LTR age for our own files
#34
juancresc
closed
5 years ago
1
output files explanation
#33
DiegoZavallo
opened
5 years ago
10
Illegal division by zero
#32
juancresc
closed
5 years ago
2
manual installation: missing modules for cpan in docs
#31
juancresc
closed
5 years ago
4
Problems running
#30
juancresc
closed
5 years ago
3
How are options given at the CLI and configuration handled?
#29
sestaton
opened
5 years ago
0
Log does not appear to express long run times correctly
#28
sestaton
closed
5 years ago
1
Tephra docker run issue
#27
mb3188
closed
5 years ago
9
INSTALL ERROR
#26
yangxiaofeill
closed
3 years ago
6
run failed
#25
ShowkyBioinformatics
closed
6 years ago
2
'maskref' command not cleaning up intermediate results
#24
sestaton
closed
6 years ago
1
Refactor fragment search to not store files for each contig
#23
sestaton
closed
6 years ago
1
findnonltrs failed
#22
altingia
closed
6 years ago
4
error in creating LTR exemplar file
#21
sestaton
closed
7 years ago
1
coordinates are reversed for some helitrons, and do not match gff
#20
sestaton
closed
7 years ago
0
Need to make one exemplar output file and clean up from 'classifyltrs' command
#19
sestaton
closed
7 years ago
1
IDs in GFF and FASTA do not match for findhelitrons command
#18
sestaton
closed
8 years ago
0
sololtr command needs optimizing for large genomes
#17
sestaton
closed
8 years ago
0
Output of 'illrecomb' command has formatting issues
#16
sestaton
closed
8 years ago
0
Incorrect coordinates in LTR-RT GFF3
#15
sestaton
closed
8 years ago
1
Need option to get age of all LTR elements
#14
sestaton
closed
8 years ago
0
LTR-RT feature clustering needs optimizing
#13
sestaton
closed
8 years ago
1
Add option to filter elements above a certain percent of N content
#12
sestaton
closed
8 years ago
0
standardize FASTA identifiers for LTR commands
#11
sestaton
closed
8 years ago
0
Try to configure emboss, samtools, hmmer3 automatically
#10
sestaton
closed
8 years ago
0
classifyltrs command output shows high percentage of unclassified elements
#9
sestaton
closed
8 years ago
0
Consider alternatives for parsing GFF3
#8
sestaton
closed
8 years ago
1
Fix threading issue with ltrage command
#7
sestaton
closed
8 years ago
2
findnonltrs command will fail with system configuration
#6
sestaton
closed
8 years ago
1
Add full working example
#5
sestaton
opened
8 years ago
0
Expand install instructions
#4
sestaton
closed
5 years ago
2
Make configuration location an option
#3
sestaton
closed
8 years ago
0
'ltrage' command not working with multiple threads
#2
sestaton
closed
8 years ago
0
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