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Hi
MGEScan seems to be a very good tool for TE annotation.
When I try to run MGEScan for a plant genome chr 2, it seems that non-LTR prog runs well.
But the LTR (find_ltr.pl) provides error outpu…
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Im running MGESCAN in my University server:
Filesystem Size Used Avail Use% Mounted on
/dev/sda4 875G 78G 753G 10% /
devtmpfs …
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Hi @oushujun,
I have been running the EDTA pipeline on several mollusc genomes to compare repeat content between species. My primary focus has been on examining how LTR content differs between prev…
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Dear:
working with Mac operating system,
```
**echo "n" | cpanm -n Data::Stag DB_File Bio::Root::Version Bio::SearchIO::blastxml Bio::SearchIO::hmmer**
Data::Stag is up to date. (0.14)
DB_F…
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Hi Evan,
Y ran tephra:
` nohup tephra all -c tephra_config.yml &`
since I want al types of TEs. I use a repbase.fasta from Solanum tuberosum for the repeatdb and left the others databases with the…
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Dear Jeremy,
The PiRATE could run RepeatScout, SINE-finder, LTRharvest, TE-hmmer, RepeatMasker. But It could not run TEdenovo, Helsearch, MITE-Hunter, MGEScan-nonLTR.
When I run PASTEC, it…
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A PiRATE user reported this error with Helsearch:
Fatal error: Exit code 1 () [formatdb] WARNING: Cannot add sequence number 1 (lcl|1_./working/GCCCTGA_CA_TCAGGGC_156) because it has zero-length. […
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trying to run MGEScan on my machine " MacOS High sierra , on eukaryotic, to detect NON-Ltr Element.
```
setup.py
File "setup.py", line 39
os.makedirs(os.environ.get("MGESCAN_SRC"), 0…
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Hi,
Can you send me the MGEScan_LTR packages you have used in this paper? I have downloaded some packages, but they did not work. Could you send me the (a modified version obtained from DAWGPAWS)…
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Hi,
I was wondering if LTR_retriever supports invertebrate genomes. We have an amphioxus genome derived from 60X Pacbio sequencing, however, it shows the LAI score is only 7.07. Moreover, all of th…