Extract reads for a specific organism classified

Hi @fbeghini
In one of my samples I got peculiar result so I want to check that is it correct. Because the particular species has relative abundance of 84% so I can blast those reads which have that particular gene which Identified that organism. Is there any way I can get to know the starting and ending point of the reads in my fastq file so that I can blast and verify that it was correctly classified? or is there any other method for the same?
I hope you understood my problem…

Secondly I had enquired in my previous issue about the viruses classified in which only the genus and species level information is provided, viruses are unclassified for the phylum to family level. why is that happening?

Thank You
Saraswati Awasthi

Hello @f.asnicar @fbeghini
There is an add-on to the two questions that I have asked in this issue, that from MetaPhlAn3 results I have made a spreadsheet more of a list of all species that a particular sample has so, now my goal is to identify pathogens from that list. Is there any database or any tool that can extract only the pathogens from my list of organisms?
I totally understand you guys are busy but I hope you find out a little of your precious time to have a look at my problem and suggest what can be done.

Thanks in Advance
Saraswati Awasthi

Yes, you could inspect the SAM file produced by MetaPhlAn and look for the starting position of the alignments of the markers of interest

Hi @fbeghini
Thanks for responding. I have one more question is --add-viruses flag updated enough to detect coronaviruses?

No, coronaviruses are not present in the database.