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Hi,
I'm wondering if there's anything I can do with a run of RepeatModeler that is taking a long time with eleredef. Is there a way to skip this step? Or to tell how long it's going to take, or wor…
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Good morning,
I'm trying to install repeatModeler and all its dependencies; I've so far compiled/installed RepeatMasker (with HMMER), RECON, RepeatScout, and TRF but I'm having trouble with RMBast:
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Hello,
I hope this tool is still actively maintained.
I was running RepEnrich2 successfully on our HPC with an old dataset in the past with the whole, unfiltered repeatmasker repeats. However, rec…
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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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Hi,
First, thank for you tools. I run the `biser` on a genome assembly with 25 chromosome-level scaffolds and 1983 short contigs (the longest contig is ~ 300kb and the shortest is ~2kb). The `biser` …
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(Copied from the lastz mailing list)
we have run lastz version 1.04.15 with --queryhsplimit=keep,nowarn:200 on two softmasked mammalian genomes. The masking comes from repeatMasker. The reason for …
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- [ ] Let's update the apollo slide deck to give a bit more time to moving around, controls, etc.
- [ ] We need to add sixpack to the GTN tutorial datasets, that'll give a better demo in some places,…
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From Monical Poelchau:
"One of our annotators is working on a gene model with ~20 isoforms. When attempting to drag more evidence into the user-created annotations track in the area of this gene mode…
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SNiPR suggests the following filtering steps:
Call/filter Variants (see EXAMPLES.sh for more information):
Step 1. Initial variant calling with GATK UnifiedGenotyper: options of -stand_call_conf 0 -st…
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Hello,
I am trying to prepare a data file for visualization using this software, but I don't understand what the score values in the 4th column of your example file (rice_MH63_repeat.bed) mean, as…