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@ValWood @kimrutherford
Hey guys,
I'll reply to your other messages shortly (sorry for being a bit tardy but it's not good time for me at the moment, I feel like am behind on everything). Here …
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I would like to understand how the output results in transposon.possible.tsv are defined. What criteria are used to determine 'all possible transposon elements'?
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I'm interested in annotating autonomous vs non autonomous transposons. Is there a means to do that in TransposonUltimate - either in the output or intermediate files? Thanks!
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Hi, I'm stuck in the pipeline with the transposon_annotation_reasonaTE module where it parses all the annotations together. I saw there were a few other similar issues, but I haven't been able to reso…
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Hi Shujun,
I'd previously used EDTA when you included MITE-Tracker (or MITE Hunter? I'm not sure which) and got some decent results for a _de novo_ yeast species. Having seen a lot of poor reports …
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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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Hi @zhangrengang
As the title, my TEsorter version is 1.4.6, I use TEsorter to classify my EDTA's outcome(my interested species is an apple species). my code:
`TEsorter Gala_genome.fa.mod.EDTA.inta…
2eYu updated
8 months ago
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Hello,
Thank you so much for developing HiC-Pro. It is a very nice tool to process Hi-C data. However, I think that there may be some limitations for analyzing the Hi-C data of organisms that consi…
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Hello. I installed gffread 0.12.1 through anaconda and used to convert a GFF3 file into GTF format.
The file I used is the gff3 annotation file from Araport11:
[https://www.arabidopsis.org/download_…
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is the new version of repeatmodele able to identify TIR, DNA Transposons?