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Hello!
Firstly,it's a imporant software truly, thanks for your creation.
Then, i have some questions about RepeatMasker. I read many introductions about this software and find that genome file(fas…
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I noticed that when I install the RepeatMasker, the path of trf is needed. I would like to know whether it is means RepeatMasker can help me to find tandem repeats and I don't have to run trf to find…
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**Describe the issue**
Many repeat coordinates hits in the ".out" file are longer than the query repeat. For example, this hit from the ".out", which is to a repeat with a consensus which is 3217bp…
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I have a working conda installation of RepeatModeler and RepeatMasker, so I wanted to install EarlGrey in the same conda environment (called “earlGrey”), following the instructions under [If you alrea…
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It is my genome.repeat.stats results:
````
total 169152450 bp sites were identified to be repeat
DNA:
CMC-EnSpm 10728 11492609
IS3EU 9 10560
MULE-MuDR …
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Hi, I've successfully run RepeatModeler and RepeatMasker to mask the genome I used, but I was confused when I checked the mask results:
* There are MULE DNA transposons in `xxx-families.fa`, like t…
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I installed `McClintock` and all dependencies in a conda environment (on the cloud; databricks) and tried the pipeline with the test dataset acquired from `download_test_data.py`. I got the following…
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Hello,
I am wondering why the .gtf/.gff file for the genome is a mandatory argument when running in 'mo' mode. It does not seem as if it is used in the shell script. Am I missing something?
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Hello again,
With your help, I was able to get chain alignments for human-mouse, human-zebrafish, etc.
I used the NCBI soft-masked genomes, and it seems like the repeat-masking was indeed not e…
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Dear Shujun,
Thank you very much for this tool.
I am doing analysis in some large genomes and TIR-Learner erros are occurring as follow:
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