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xunchen85 / ERVcaller

ERVcaller is a tool designed to accurately detect and genotype non-reference unfixed endogenous retroviruses (ERVs) and other transposable elements (TEs) in the human genome using next-generation sequencing (NGS) data. We evaluated the tools using both simulated and real benchmark whole-genome sequencing (WGS) datasets. ERVcaller is capable to accurately detect various TE insertions of any lengths, particularly ERVs. It allows for the use of a TE reference library regardless of sequence complexity, such as the entire RepBase database. It is easy to install and use with command lines.

Home Page:http://www.uvm.edu/genomics/software/ERVcaller.html

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Some chromosomes don't harbour any variation

1577377232 opened this issue · comments

commented

Hello, Dr. Xun Chen,

I would like to ask how to use Order_by_TE_sequence.pl? The species I study is chickens, 1 to 39, Z, W, MT. Or how can I change the chromosome names？

Dan

commented

Hi Dan,

Have you try running the latest ERVcaller from this repository? The updated script should be able to handle it.

If it doesn't work, you could also simply add those chr IDs to the script as the same as others. I could also help if you send me the full chromosome IDs.

Thanks,
Xun

commented

Hi Xun，

I succeeded in getting the desired result according to your prompt.
Thank you very much! Wish you a happy life!

Dan