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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.
http://www.uvm.edu/genomics/software/ERVcaller.html
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I also had a problem with the second step #20

Open wuzhiwei-sys opened 11 months ago

wuzhiwei-sys commented 11 months ago

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.) image image

xunchen85 commented 11 months ago

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

wuzhiwei-sys commented 11 months ago

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? image image

xunchen85 commented 11 months ago

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

wuzhiwei-sys commented 11 months ago

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

wuzhiwei-sys commented 11 months ago

image

xunchen85 commented 11 months ago

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

wuzhiwei-sys commented 11 months ago

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

wuzhiwei-sys commented 11 months ago

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

xunchen85 commented 11 months ago

nice, let me know if you have further questions.

Xun

wuzhiwei-sys commented 11 months ago

yeah！Thank you！