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What is the difference between the 'Phages, Prophages, Transposable elements' and 'Phages, Prophages, Transposable elements, Plasmids'. How are 'Phages, Prophages, Transposable elements' incorporated …
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## Problem description
I want to discover TIR (Terminal Inverted Repeat) elements with gt tirvish. I ran the command as I show you next (without problems). Then I want to filter the output by protei…
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Hello, Yesterday I 've installed successfully salmonTE but I need to create a new index because I have a library of transposable elements of my species. The problem is that I cannot create the index b…
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Dear Xun Chen,
Hi. I'm Oh.
I have three questions.
1) In your programs, there is no process using "Hydra". Is it right?
2) Where can I find "TE_consensus.fa" in your user manual?
3…
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Hello TEtranscripts group,
My question is not in the main part of TEtranscripts process (it works fine since you helped me last time, and thank you for that), it is in the alignments preparation.
…
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I was trying to use TEtoolkit to quantify signal at transposable elements from a chromatin accessibility assay (ATAC-seq). At first, I tried aligning the ATAC-seq data with BWA aln/sampe, removing dup…
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Hello,
So I've a slight issue. I want to predict genes. the species is duck. but the "final_training_models.gff3" file seems missing. The snap and glimmer software can not find the final_training_m…
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```
TEcount -b /SAN/vyplab/alb_projects/data/muscle/analysis/STAR_aligned/6_27_4_18.Aligned.sorted.out.bam --sortByPos --GTF /SAN/vyplab/vyplab_reference_genomes/annotation/human/GRCh38/gencode.v31.n…
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Hi,
Sorry for the interruption. I just want to know if there is any guideline for reformatting downloaded UCSC TE GTF file? I found the discussion [here](https://github.com/mhammell-laboratory/tet…
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Hello there,
Quick question, how does bwa-meth handles reads multimapped?, for examples, reads mapping to transposable elements.
Cheers,
Luis Alfonso.