SQMTools Error Error in subsetORFs

[johnbio12]

Error in subsetORFs(SQM, goodORFs, tax_source = "contigs", trusted_functions_only = trusted_functions_only, : No ORFs were selected. Perhaps the subset query yielded no results?

I wish to know whether I can use one bin from the above list of bins. Or how to select a specific bin at this step.

maxbin005 = subsetBins(Hadza, 'maxbin.005.fasta.contigs' )

Plot functions

plotFunctions(maxbin005, fun_level = 'KEGG', count = 'tpm')

contigs must be in path or only the name is enough.

[fpusan]

I am not sure of what your issue is exactly? maxbin005 = subsetBins(Hadza, 'maxbin.005.fasta.contigs' ) This should indeed work as long as maxbin.005.fasta.contigs in indeed one of the bins in your the object Hadza.

[johnbio12]

The issue is in my case maxbin not generated rather I have only metabat2 and concoct2. But provide metabat2 gives error

[fpusan]

This will work with the bins that are present in your dataset. You can check which ones are in there by looking at the bin table SQM$bin$table

[fpusan]

Closing due to lack of activity, feel free to reopen