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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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RNAseq data #19

Open hkoo87 opened 1 year ago

hkoo87 commented 1 year ago

Hello, Thank you for sharing the ERVcaller.

I was wondering whether this tool can be used for single cell RNAseq data sets (fastq format).

Any suggestions will be appreciated.

xunchen85 commented 1 year ago

I haven't tried it, but ERVcaller was designed to detect polymorphic TE insertions. If you want to look at single-cell ERV expression, you could look at other tools, like scTE, https://www.nature.com/articles/s41467-021-21808-x

Thanks, Xun

hkoo87 commented 1 year ago

Thank you for your suggestion. I was able to install and successfully run the test data set.

I tried to replace TE_consensus.fa file including my interest genes, however I kept getting an error message as below:

[E::bwa_idx_load_from_disk] fail to locate the index files
Use of uninitialized value $std_insertsize in concatenation (.) or string at /data/user/home/ERVcaller/ERVcaller-1.4/ERVcaller_v1.4.pl line 975.

I was able to see bam, bam.bai, and fq files were successfully created, however just the vcf file was not able to be generated.

Could you give me any suggestions on this?

Thank you.

xunchen85 commented 1 year ago

Hi,

It usually indicates empty results. Could you check the intermediate results? e.g., *ERV.output2 or ERV.output3?

Also, did you use single-end FASTQ as the input? It was also strange that the insert size was not computed.

Thanks, Xun