I have made run several metagenomic samples through Baqlava and keep seeing VGBs in the tempfile_markers.txt file that don’t show up in the profile files. Shouldn’t every marker that has a hit show up in the profile file?
Hi Che! Thanks for asking! The tempfiles (markers & ORFs) will show every marker and ORF mapped to, before any filtering has taken place. BAQLaVa carries out a number of filtering steps to make sure the final BAQLaVa profile is the most accurate view of viruses present in the sample. VGBs which are observed in the tempfile but not in the BAQLaVa profile are because we do not have enough evidence to support prediction of that VGB really being present (whether due to low coverage across a VGB’s set of markers, or because the initial mapping takes place at very low marker coverage thresholds, which we then filter more stringently downstream). In any case, it is not a concern that you are seeing VGBs in the tempfile that do not make it to the final BAQLaVa viral profile. Let us know if you have any other questions!
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