-
Hi,
Are the .gtf and the prebuilt_indices are somehow related ?
I download both and I got different annotations:
https://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/T2T…
-
Hi EVM team,
Thank you very much for this wonderful tool.
I am annotating a plant genome (~500 Mb), that has ~50% repeats that was masked by RepeatMasker. For annotation, I used a soft-masked geno…
-
**Description:**
Click to expand for Sample of processing error
```
Successfully created the directory
/TELR/intermediate_files/vcf_ins_repeatmask
RepeatMasker version open-4.0.7
Searc…
-
Hello,
During the past couple weeks I tried to run several Detection steps with the PiRATE pipeline and all of them reported the same error. It is about invalid characters in the fasta file. Below …
-
---
Author Name: **fanshaohua empty** (fanshaohua empty)
Original Redmine Issue: 2909, https://redmine.open-bio.org/issues/2909
Original Date: 2009-09-08
Original Assignee: Bioperl Guts
---
The rep…
-
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 …
-
Dear @oushujun ,
Thank you for developing this useful tool. I have run it successfully and found that SINEs and LINEs could't be identified based on structure features. However, we didn't have such T…
-
**Are you using the latest release?**
1.8.15, installed via mamba
**Describe the bug**
In stdout, masking seems fine:
```
OS: Ubuntu 20.04, 64 cores, ~ 528 GB RAM. Python: 3.8.15
Running funan…
-
In RepeatMasker/4.1.2-p1, they've changed their database filetypes from `.embl` to `.h5`. And masker is checking for `.embl` files before it runs.
Add a check for `.h5` files on line 4972 in `lib/…
-
Regarding "AmpliCoNE usage with other reference genomes / species". Under step 1, it indicates that output from RepeatMasker and Tandem Repeat Finder are needed.
I'm using a new assembly, and those…