-
Add TIR extraction module from TE-Splitter as additional TIRmite cmd line tool.
Function: Find and extract TIRs from DNA-transposons or MITES
-
Hello,
I performed an annotation of my genome (N50 = 326 kb) with BRAKER with RNA-Seq. Repeats were softmasked with RepeatModeler + RepeatMasker and the RNA-Seq data was aligned to the softmasked g…
-
When running EDTA_raw.pl script the output for both TIR and Helitron raw fasta files are empty. I think the problem is at the call_seq.pl script because the TIR.ext30.list gives an output such as:
…
-
Hi Shujun,
Is there any method to further classify the DNA transposon that name as DNA/DTT, DNA/DTA by EDTA into specific superfamily names such as Harbinger, Mu, AC/DS and others?
Best regar…
-
- [x] _A. ricciae_ The problem:
> Something is also wrong with the TE level for A. ricciae in figure 4 and main text, which is much lower than the other bdelloid rotifers – but they show similar le…
-
Hi Sabastian,
I couldn't find usage page on the release page.
In the tar ball I downloaded, there's the .cpp file but it doesn't have any usage messages I guess?
Do you have an example showing how …
-
Hi Evan,
Thanks for this tool. I wanted to report an error running the tephra age command to estimate tir age. I'm running this in a docker container. Here is the error:
> Can't use an undefin…
-
Hello,
I am trying to run Tephra for the first time using your Docker container. I ran silent run using nohup
in expectation to produce gff file for my assembly
nohup tephra all -c tephra_confi…
-
Hello! I was looking through SalmonTE's references and noticed that their clades don't seem to have all of those listed in the "clades_extended.csv" file. It would just be really nice if all of the …
-
Hi,
Hi, I'm getting an error running the following command in PASA:
`perl Launch_PASA_pipeline.pl --config alignAssembly.config --ALIGNERS blat,gmap --create --run --genome genome.fasta --CPU 20…