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wejlab / MetaScope

An R-based approach for preprocessing and aligning 16S, metagenomic, and metatranscriptomic data (PathoScope version 3.0)
GNU General Public License v3.0
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metascope_id() output: column header definition #25

Closed esraagithub closed 7 months ago

esraagithub commented 7 months ago

hello thank you for your great tool could you please define the columns header (read_count , Proportion, readsEM, EMProportion) in the resulted csv file from metascope_id () function? Also i want to know the %identity of alignment if possible.

aubreyodom commented 7 months ago

Hi,

read_count = Number of reads assigned to the genome Proportion = proportion of the total reads identified made up by the given genome readsEM and EMProportion are related to the EM step, and essentially should be similar in output to read_count and Proportion, but these are otherwise unused in calculations.

%identity of alignment isn't automatically output. You could get a sense of it looking at the BAM file from the filter step, but the reads aren't assigned until the EM in the metascope_id() step and there's no updated alignment file output, so this is imperfect.

Thanks, Aubrey