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Hi @HajkD,
I keep getting this error in the filtering step just before usearch clustering.
Which file is failing to be parsed at this stage?
```
Input: /disk2/nguinkal/Zander_Project/pipelines/L…
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list generated back in 2013:
Study ERP002090 (CENP-A (Cnp1)) AE
Study SRP019199 (Schizosaccharomyces pombe fission yeast deletion library barcode sequencing)
Study SRP005690 (Schizosaccharomyces …
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Hi,
I'm trying to explore the TE content in mosquitos genome. As for as I understand the EDTA pipeline with developed to work with plant species and was inspired by this [guide](http://weatherby.gene…
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**Submitting author:** @HajkD (Hajk-Georg Drost)
**Repository:** https://github.com/HajkD/LTRpred
**Version:** v1.1.0
**Editor:** @lpantano
**Reviewers:** @dcassol, @mdozmorov
**Archive:** 10.528…
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**Submitting author:** @HajkD (Hajk-Georg Drost)
**Repository:** https://github.com/HajkD/LTRpred
**Version:** v1.1.0
**Editor:** @lpantano
**Reviewers:** @dcassol
**Managing EiC:** Lorena A Barba
*…
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Dear Shujun,
Thanks for developing LTR_retriever. I used LTR_retriever to annotate a subset sequences of a plant genome and found 2333 intact LTR-RTs. This number is much less than that annotated by …
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I hadn't seen
heterochromatin domain assembly before
The aggregation, arrangement and bonding together of a set of components to form a heterochromatin domain.
how does this differ from the parent…
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Personally, LTR_retriever is developed primarily to assess plants genome assembly quality. LAI requires a minimum of 5% total LTR and 0.1% intact LTR sequences present in the genome for the purpose o…
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In the *.cls.tsv file, the header is listed in the following format. However, in the place of "Order", the true classification should be in the "Subclass" level. For the order level, it probably shoul…
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Hi,
I am assembling a heterozygous 2.5 Gb (haploid size, so we expect a ~5 Gb assembly) plant genome. We have about 35x coverage per allele and many copies of a very few repeats (LTR-retrotransposons…