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import itertools
with open('work.txt', 'w') as w:
f=open('fast.txt', encoding='utf-8')
for i in f:
tem = "RepeatMasker -nolow -no_is -norna -engine ncbi -parallel 4 -lib …
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Some G repeats have a high quality score and are annotated by RepeatMasker with a category. But, it's quite similar to no-calls.
```
chr1 1902198 gridss0f_7215b G GGGGGGGGGGGGGGGGGGGGGG…
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If all rounds of RepeatScout + RECON succeed but LTRPipeline fails, then using the `-recoverDir` option will claim that the directory contains a successful run. Since merging the results of the two me…
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hello there,
After running successfully the tool until Squire Count, yay! I was going over the Count output tables and I noticed that the same individual (Same TE family, same Chrom:Start-END) was d…
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We've observed that Mutator transposons annotated by RepeatMasker often overlap with part of the exons in a gene, meaning the exons frequently become part of the internal sequence of Mutator. However,…
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RepeatModeler/RepeatMasker are extremely heavy on the file system i/o. We will likely get a complaint from the HPC admin to run it as it is implemented for now.
The problem is that these tools requ…
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I have been running the most recent conda release of RepeatModeler which runs smoothly until round 6. The RepeatModeler job completes, but the LTR Structural Analysis never runs.
LTR Structural Ana…
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- [x] Map all reads to reference (from Broad institute), look for coverage peaks
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Thank you for sharing the code. I really appreciate it.
I have a few questions:
1) how do you define SUNK using Jellyfish (I assume)?
2) what does `parentRead` here https://github.com/glogsdon1/su…
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Hi Shujun,
This is not a bug report, but a question. I've noticed that when I run EDTA on Drosophila genome, it takes an extraordinary amount of time when searching for LINEs. Drosophila genome is …