Scott Teresi

icon indicating a website link https://polyploidy.msu.edu/ icon indicating an email [email protected]

icon company Michigan State University icon location Lansing, MI icon location PhD student in the Edger Lab at Michigan State University. Author of TE Density.

Results 7 issues of Scott Teresi

Use of unitialized value $chr_pre in has element call_seq_by_list.pl line 87

3 comment

Hello Shujun, I was running EDTA v2.0.0 on a small cranberry genome and got the following error: `Use of uninitialized value $chr_pre in hash element at /mnt/home/teresisc/anaconda3/envs/EDTA/share/LTR_retriever/bin/call_seq_by_list.pl line 87.` The...

PanEDTA Line Detection

7 comment

Hello Shujun, Hope you are doing well. I am writing to share that I had issues with LINE detection in PanEDTA. I am hoping that this will help anyone else...

Output data analysis: Make table generation more robust for people with fragmented data

# Purpose: Make the helper function `add_te_vals_to_gene_info_pandas()` within `density_utils.py` more robust to requests for TEs that are not on that particular HDF5 file. # Context: **This is not main pipeline...

Refactor MergeData manager out of process_genome.py

How to interpret the process density progress bar

@teresi Can you please explain how to interpret the TE density progress bar numbers? For example when it is calculating density it will say `subsets:` show a progress bar and...

Unclear Error Message for "Old" Overlap Values.

1 comment

Error: "The windows for MergeData do not match with the windows of Overlap" Described in `transposon/merge_data.py` under `_validate_windows` function Easily occurs when there are previously calculated Overlap files on disk,...

enhancement

Unusual Output and Failure During Regular Annotation

Hello Shujun, I am running the latest EDTA from the master branch 41cd64f and I am getting an error with 1 out of 3 of my genomes. I have looked...