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I am running LTR Retriever as a part of RepeatModeler. RepeatModeler sets each dependency manually on the command line, including the -blastplus parameter. But LTR Retriever is looking in some other d…
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> parse
@mhemberg
Hai did you get restults by running these comments
"singularity exec docker://dfam/tetools:latest BuildDatabase -name sequence_index -engine ncbi sequence.fa…
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[code](https://github.com/urol-e5/deep-dive-expression/blob/main/D-Apul/code/14-Apul-RepeatMasker.Rmd)
I'm trying to run RepeatMasker to id TEs in our E5 coral genomes, and have been using [Sam's scr…
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Hi,
Thank you very much for developing this tool！
I find some regions motif edit distance is too large:
`chr1 7105232 7105273 GAGCTGG,GAGCCAA,GGGCTGG,GAGCTGC,GAGCTCT,GAGCTG`
"GAGCTGG","GAGCCAA"…
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**Describe the issue**
Trying to run the LTR Pipeline alone to add to some libraries and then re-mask some genomes. So far, this is only happening with one genome. I use the -LTRStruc flag for Repe…
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Is it possible to use SQuIRE with a non-model organism by providing the genome assembly in FASTA format and the Repeatmasker output files (.tab, .tsv) instead of running fetch? And which files and Rep…
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Hi Professor Ou:
I would like to ask whether I can concatenate EDTA library and Repbase library, then run RepeatMasker manually? I was glad to find EDTA can significantly reduce the percentage of u…
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Having an error message which persists after a restart using
```
TOIL_SLURM_ARGS="--partition=macmanes --exclude=node116,node115" \
cactus $HOME/jobs2 $HOME/final_cactus_input.txt mammals2.hal \
…
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- Run RepeatMasker program to find repeated sequences (use fungi as species)
- https://github.com/fmfi-genomika/genomika-2017/wiki/RepeatMasker
- RepeatMasker and repeat library installed at compbio…
mrshu updated
6 years ago
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this is the error I am getting while running:
wget --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-co…