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**Describe the bug**
Many repeat coordinates hits in the ".out" file are longer than the query repeat.
For example, the line below is data is from the ".out", which a hit is to a consensus repeat …
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Hello, thank you for developing the TE annotation software "EarlGrey." It makes annotating transposable elements very convenient. However, I have some questions. My species is a non-model plant, and c…
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Hi @rnakato,
I am currently learning to use the programs included in the `ssp_drompa` Docker image and have a couple of questions about `drompa_peakcall`:
1. Should the value assigned to `-wid…
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So I have 2 queries, 1st, does earlgrey require an internet connection whilst running? One of the first messages printed looks like it is for downloading Dfam_curatedonly.h5.gz, this will be a problem…
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Error message
```
Reading the RepeatMasker EMBL file: RepeatMaskerLib.embl
Warning...unknown stuff <
>
```
refers to the following process in **prepRepeatMaskerDB**
https://github.com/Kristin…
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Hello Shujun,
Curious if the TIR elements identified using "EDTA_raw.pl --type tir" requires filtering. Its generate two files *.intact.fa and *.raw.fa, both of which are same. Does this indicate tha…
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I followed instructions on https://github.com/Dfam-consortium/TETools#readme to add Repbase. After I set LIBDIR to the new Libraries directory, can RepeatModeler/RepeatClassifier pick up the LIBDIR v…
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Hi Toby,
I am trying to run earlyGrey (by conda installed) with two genomes. one genome is small (200Mb) and the other one is big (1.3Gb).
When running it with the big genome, I got errors. I g…
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Hi,
I've run Earlgrey on >100 Drosophila genomes with default parameters. I'm masking annotated protein coding genes that are in the known repeat rich regions using the filtered repeats gff/bed file…
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Hello,
I am using EDTA v2.2.0 to process my insect genomes. The commands looks like this:
`EDTA.pl --genome ${genome.fa} --species others --step all --overwrite 0 --sensitive 1 --anno 1 --threads…