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When using HiTE, I encountered KeyError using different genomes. Hope to get your answer.
Script:
#!/bin/bash
source ~/anaconda3/bin/activate HiTE
python /work/home/qljgroup02/01.chinese/01.wg/s…
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Hi!
Thanks for developing dante_ltr. I tried to run dante and dante_ltr on a genome but received an error message during the dante_ltr step.
I ran dante and dante_ltr with the following commands…
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Hello!
In TEanno.gff3, TE_00000019 actually has multi-locus repeats on each chromosome, so do these TE_00000019 need to be merged and spliced again? Or do these transposons already contain the full L…
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**Reported by davpabenwo on 2012-02-20 12:19 UTC**
To allow for the classification of a non-genomic coding/pseudogenic gene structure.
I guess these would have to be child terms of CDS and also child…
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I would like to use the pipeline on a large plant genome. Would it be to run separately on chromosomes or directly on the entire genome? Are there any requirements for CPUs and RAM? Have you ever test…
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Hi,
I would like to know whether the "Total interspersed repeats" percentage in the tbl output file is the sum of the "Retroelements", "DNA transposons", "Rolling-circles", and "Unclassified". When …
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```
2024-08-14 20:37:50,275 - main.py[line:406] - INFO: Start step0: Structural Based LTR Searching
2024-08-14 20:37:50,275 - main.py[line:419] - INFO: cd /home/pxxiao/tools/HiTE/HiTE/./module && py…
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Hi,
I found that there are always too many LTRs no matter what sequences I provided.
For example,
1) helitronscanner(https://sourceforge.net/projects/helitronscanner/) results as input,
![imag…
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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
10 months ago
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- [x] Download the Genome from NCBI
GCF_000767585.1_PRJNA234474_Ca_dromedarius_V1.0_genomic.fna.gz`
### LTR-Detection
- [x] **Create index** _find pairs of maximal exact direct repeats that a…