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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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I also had a problem with the second step

wuzhiwei-sys opened this issue · comments

commented

Hello, Dr. Chen, I have the following problems when using the test data. May I ask how I can solve them? (I have the same problems when I use my own data.)
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commented

Hi, I think you forgot to put the number of CPUs for "-t", like "-t 10". Also "-I" is for the folder containing the FASTQ files and "-O" for your output folder.

Thanks,
Xun

commented

Prof. Chen, thank you very much for your reply. However I still have the same problem when running the code. Then how can I solve it?
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commented

Hi,

Have you run the test data yet? Btw, have you installed SEI-MEI successfully? if not, you could follow the steps in README. could you also show a list of files under the output folder?

Thanks,
Xun

commented

yeah，SEI-MEI should be installed successfully.like this:
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I tried the test data, but the same error was reported. Then ran my own data.
the output/ file is as follows：
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commented

Hi,

I would suggest you run it with the test data first and then apply it to your datasets.

Few suggestions and tips for testing the tools:

  1. please export the paths of all included tools, including SEI-MEI (see README file).

  2. all references should be indexed with bwa, including the human reference genome and TE reference genome (see README file too).

  3. ERVcaller would support human chromosome IDs, such as "chr1", "chr2" and so on. If you are working on other species, you could try rename them.

Best,
Xun

commented

Okay, thanks again for your reply. I will try it again. Best wishes to you!!

commented

Prof. Chen, I successfully ran the software by modifying the reference genome. For other species, chromosome number modification is a must. ERVcaller works great!！！

commented

nice, let me know if you have further questions.

Xun

commented

yeah！Thank you！