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Hello,
I am not able to complete a RMasker run, the error I get is the following:
```
WARNING: The search engine returned an error (134, status = 134 )
Engine parameters: /cluster/apps/gdc/rmblast…
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Need options around using a GFF file of known transposons for the reference genome.
- Tag clusters/insertions as known vs unknown
- Used as additional information for joining clusters #78
- Used f…
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The current hierarchical clustering algorithm works well under most circumstances. However it can lead to excessive-splitting around regions of densely nested transposons (i.e. Gypsy elements in centr…
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Hi Adam,
I tried to spike-in one indel per size [149, 1000] bp in my 151 bp read WGS BAM.
```
python $addsv -v $svs -f $bam -p 8 -r $fasta --aligner mem -o $o
```
According to the VCF I g…
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For PomBase annotation extensions (e.g. GO & phenotype), we could use a term for RNA transcribed from long terminal repeats, such as:
name: long_terminal_repeat_transcript
def: An RNA that is transcr…
mah11 updated
6 years ago
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from https://github.com/pombase/curation/issues/1960
I wanted to re-run the pombe data with the gaf from 28 April, ex- PAINT data. I have now done that.
The results are:
707 unknown
0 unannota…
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This is more a conceptual question regarding roary than an issue with the software, so please excuse me if this is not appropriate here:
How exactly does the paralog splitting work in roary? In the p…
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Note: all of the species tests have (I think) an implicit bug where they will fail to do the right thing when viewing results for the Hawaiian strain (c_elegans_PRJNA275000), assuming there are ob…
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I think most of the query types are quite simple but I think it would be more friendly to have a one sentence title or description above each type. For example the "Coding exons" type could have some…
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- [x] exclude dubius
- [x] exclude transposons
That will probably do it. The other issues are related to GO, or curation. I'm working on reducing the number which do not map to the slim today.…