Missing phage genome in SRA metagenomic data

Question

[mendonca_thiago22]

Hi all, I have 3 metagenomic assembled phage genomes from NCBI with their respective SRA reads downloaded. I just want to confirm the presence of these viruses in these SRA files. I was able to do that to 2 of them by just building the scaffolds with Spades (metaviral mode). I'm having trouble finding the third virus in its respective SRA data, I've tried: Spades, Bowtie (mapping the reads to the assembled genome) and VirSorter with no results. I do not know if I could do something else or there is some kind of error in the information provided by the NCBI. Any clues?

Answer 1

[Matthias Zepper]

Sounds like a pretty thorough investigation to me. If there are no reads mapping to the assembled genome that was supposedly created from those reads, I would consider this highly suspicious and suggestive of an error in the database (e.g. the wrong file was submitted to SRA by mistake).

The only alternative explanations that come to my mind: You happen to be interested to find back Phi X 174 or some mapping issues that can be fixed with different settings (reads need to be quality-trimmed, RNA/DNA conversion required?). But at this point, I would also start considering a database error, in particular, since you could identify the other two phages.

[mendonca_thiago22]

It seems like a database error indeed

[GenoMax]

Consider emailing SRA support and the submitter's with relevant information. This may get fixed eventually.

Answer 2

[GenoMax]

You could do a blast search against SRA (you can only do this via NCBI web blast page) with that last phage and see what you get.

[mendonca_thiago22]

Just tried that, had positive hits but with percentage identity below 100. No hits when using as query the phage gene that I'm investigating. Positive 100% percentage identity hits for the same gene from the other two phages in their SRA runs though