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Hi!
I am trying to use RepBase as the default database for RepeatModeler / RepeatMasker, however, I am running into an issue. I am currently using the Docker version of the software (dfam/tetools).…
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Hi @andrewgull
I've tried to setup the described environment from scratch, but the configuration process took too much of my spare time.
So for the second time I've tried to use `conda` for setup…
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Hi , thanks for your scTE !!
Now I want to use the scTE_build command to generate the annotation file, but my TE file is the repeatmasker generated .out file. I have noticed that TE needs to be i…
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My current best and quickest solution for retrieval of repeat annotations is to make the RepeatMasker download link configurable via the `config.yaml`. However, this has several restrictions:
1. It…
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hello, I would like to ask a question about your TE annotated script.
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RepeatMasker -pa 24 -div 22 -cutoff 250 -gff -lib barthiiSpecificTelib.fa -nolow -norna -xsmall barthii.fa
Where is the …
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singularity run --nv /home/liux/miniconda3/envs/braker3/helixer-docker_helixer_v0.3.2_cuda_11.8.0-cudnn8.sif Helixer.py --fasta-path /home/liux/DATA/genomic/RepeatMasker/AT/TAIR10_chr_all.fa --lineag…
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Hi,
I would like to use CASK and I have started with the database creation. Apart from problems with RepeatMasker input that I was able to solve myself (the script is not suitable for minor changes…
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**Describe the issue**
*I am running the RepeatModeler on a ~900 Mb fish genome. The job was completed successfully and I got the families.fa and families.stk files. But at the same time I also got…
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Hello,
I have a question about FUNGAP running, is there any way to give FUNGAP a previously masked genome to run it and avoid this step? Or give to FUNGAP a pre-made custom repeat library to run wi…
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Dear Kevin,
You did not recommend users to use the conda packages of these tools; however, since I am not familiar with RepeatMasker and
RepeatModeler, I used conda packages of these tools.
…