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Grice-Lab / HmmUFOtu

An HMM and Phylogenetic Placement based Ultra-Fast Taxonomy Assignment Tool for 16S sequencing
GNU General Public License v3.0
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Filter question #4

Open pamelacamejo opened 5 years ago

pamelacamejo commented 5 years ago

Hi,

I run the following command to classify some 16S amplicon sequences:

hmmufotu gg_97_otus_GTR unmapped_otus_rev.fasta -s 0 -t 0 > hmmufotu_gg_97_unmapped.out

I noticed that some reads have very poor alignment coverage with the database, and even that, they have a taxonomic assignation. Do you recommend to use any filter for taxonomic assignation after running hmmufotu?

e00011027 commented 5 years ago

Hi,

Looks like you are trying to map some unmapped reads. First make sure you have the latest HmmUFOtu installed, and second make sure HmmUFOtu guessed your 16S read orientation correctly. Sometimes 16S primers are miss labeled some forward reads are reverse reads and vice versa.

If everything is OK you could try to filer reads in the hmmufotu-summ step. There are a few identity options and try something like 0.5 is reasonable.

Best Qi

On Tue, Jun 25, 2019, 2:31 PM pamelacamejo notifications@github.com wrote:

Hi,

I run the following command to classify some 16S amplicon sequences:

hmmufotu gg_97_otus_GTR unmapped_otus_rev.fasta -s 0 -t 0 > hmmufotu_gg_97_unmapped.out

I noticed that some reads have very poor alignment coverage with the database, and even that, they have a taxonomic assignation. Do you recommend to use any filter for taxonomic assignation after running hmmufotu?

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