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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?
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Some additional comments on how to interpret the data were made In the meeting with Werner.
- There is a sequencing bias in the number of reads. We probably cannot do anything about this, but the s…
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Hi, rmhubley
The results of version 4.1.5 (Dfam 3.7) compared to version 4.1.3 (Dfam 3.6) for the same species clearly have a higher proportion of the former masked, is this normal? Also, I compare…
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This looks like a great resource! I'm looking at prokaryotic transposons and I'm interested to know if MITE-Tracker has ever been tried on larger, autonomous, class II TEs? And specifically whether sp…
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Dear @sean-bam ,
Thanks again for a great analysis and resource!
I am interested in examining the sequences/data associated with clade4 of the phylogenetic tree. In the manuscript, clade 4 includ…
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I am running HISAT 2.0.5 and working with the Arabidopsis thaliana annotation [Araport11](http://www.arabidopsis.org/download/index-auto.jsp?dir=%2Fdownload_files%2FGenes%2FAraport11_genome_release), …
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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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**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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Hi,
I found that there are many Plantae sequences and just a little Animalia sequences in TransposonDB.fasta, is that normal?
grep ">" TransposonDB.fasta|wc -l
891052
grep ">" TransposonDB.f…