Can not map the viruses after running the UMI-tools

[loubean4073]

Hi, thank you for your great work! There is a problem when I use UMI-tools to deal with the fastq files. If I just run the scanning script with the fastq without pre-processing by UMI-tools, I can map several viruses from the QC file shown. But after running UMI-tools(stop at step 3) to get the extract fastq, there is no virus to be mapped. Does this have anything to do with setting parameters in UMI-tools?

Thanks Dequan

[PierreBSC]

Hi Dequan,

That's indeed pretty weird. What kind of viruses do you get when applying VT on the raw data ? How many reads do you get for those hits ? Can you send me the QC text file produced using the raw and filtered data ? Best Pierre

[loubean4073]

Thank you for your reply. Here are the two text files(the raw and filtered data) without pre-processing by UMI-tools. QC_unfiltered.txt QC_filtered.txt

[PierreBSC]

Hi Dequan,

So I have looked at the QC you sent me. Basically there is no virus with a very clear signal in the QC_unfiltered file. The only viruses with a decent quality (in term of coverage and sequence entropy) are also found in the filtered one, and in a very low amount (<100 reads uniquely mapped). It just seems that : 1) There is no real viral infection 2) The artifactual reads are removed upon processing by UMI tools ! Hope this helps, Best Pierre

[loubean4073]

Hi Pierre, Thanks a lot for your help to analyze the cause of the problem, I will try later by replacing the other fastq files. Thanks a million again!

Best Wishes Dequan