Hello All,
I would like to start a pipeline to analyse 16S RNA data, however I am not sure weather to include the step of removing duplicates or not. The aim of metagenomics is to compare different samples and see how the microbiota is different within samples of different conditions/time points.
After aligning, each sequence will match a sequence from a database, which will be then mapped to a bacteria and assigned taxonomy. the aim is to find how microbial content changes within each sample. If I removed duplicates, each sequence will be represented once, then taxonomy to this organism will be assigned once! so I am losing data here, which is the content of unknown bacteria in a sample with quantity for each one.
I am not sure if I am perceiving this right or not! I appreciate your comments.
Regards,
Bioinfguy
I would like to start a pipeline to analyse 16S RNA data, however I am not sure weather to include the step of removing duplicates or not. The aim of metagenomics is to compare different samples and see how the microbiota is different within samples of different conditions/time points.
After aligning, each sequence will match a sequence from a database, which will be then mapped to a bacteria and assigned taxonomy. the aim is to find how microbial content changes within each sample. If I removed duplicates, each sequence will be represented once, then taxonomy to this organism will be assigned once! so I am losing data here, which is the content of unknown bacteria in a sample with quantity for each one.
I am not sure if I am perceiving this right or not! I appreciate your comments.
Regards,
Bioinfguy
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