Konstantinos Gidiotis

icon company Centre for Research in Agricultural Genomics icon location Barcelona, Spain icon location Junior Bioinformatician at CRAG

Results 4 issues of Konstantinos Gidiotis

Using RagTag to close the gaps in a chromosome or reference genome using long-read data

Hi, So I have a draft-genome assembly assembled with short-read data and with many repeptitive and uncharacterized regions. Moreover, I have low coverage (9x) long-read data recently generated from a...

How to interpret variation graphs in SequenceTubeMap

Hi vgteam, This is my first time using SequenceTubeMap and vg and I want if possible to explain to me the following figures. I did generate a vg (variant graph)...

Clarification on EDTA output: differences between `intact.fa`, `intact.gff3`, and `raw.fa`

I’m working on detecting intact LTR retrotransposons in a specific chromosome using EDTA. The goal is to understand which output file represents the final set of intact LTRs for downstream...

timeout -s KILL 300s and Error: Error while loading sequence

3 comment

Hi, and thank you for this great software. I’m working with a plant genome and I’ve encountered some issues related to EDTA_raw.pl and LTR_retriever. I have the following error: ```...