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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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Error in finding the input data under the provided sampleID #33

Open ChrisMimir opened 6 months ago

ChrisMimir commented 6 months ago

Hi, Many thanks for developing this tool. As shown in the screenshot, I met the issue in "finding the input data under the provided sampleID", no matter by using my own data nor the test data provided in this tool.

image

I am not sure about the cause, could you do me a favor in solving it?

Additionally, many warnings jumped out when I was installing SEI-MEI under the Scripts folder, is it normal? Though the SEI-MEI installation seemed to be finished without interruption. If possible, could you make ERVcaller a docker image, that would be helpful.

Best regards, Chris

xunchen85 commented 6 months ago

Hi Chris,

The installation of SEI-MEI should be okay if the extractSoftclipped command under the SEI-MEI can be run. The error should be due to the path issue. From your command line, I think you should specify the folder containing the input files and then add the full paths to the reference genomes first. Please also check if the fastq files are present in the folder too.

Overall ERVcaller should be easy to install and use. Also thanks for your great suggestion, we may prepare a docker image for a newer version too.

Xun

ChrisMimir commented 3 months ago

Thank you so much for replying. The issue has been solved under your instruction.

Best regards, Chris