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epi2me-labs / wf-metagenomics

Metagenomic classification of long-read sequencing data
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non-assigned reads #76

Closed HannahBenisty closed 10 months ago

HannahBenisty commented 12 months ago

Ask away!

Hi, I am looking at 16S rRNA gene sequencing data and I would like to know if there is a way to know the percentage of non-assigned reads per sample. Thanks!

nggvs commented 11 months ago

Hi @HannahBenisty ,

non assigned read appeared in the report as Unclassified, you can calculate the percentage from that. Is there anything that you have found weird?

Thank you!

HannahBenisty commented 11 months ago

In the report I do not find any "unclassified" and I was surprised about that. Thanks

nggvs commented 11 months ago

Are you working with environmental samples? From which environment? Also which pipeline were you using (kraken2 or minimap2?) I'll take a look just in case

HannahBenisty commented 11 months ago

yes, environmental from freshwater. I am using minimap2

nggvs commented 11 months ago

Oki, thank you! Also, if you could tell me which version are you using or if you are running a specific parameter I would appreciate it

nggvs commented 11 months ago

Hi @HannahBenisty , I have reviewed this. Could you run the workflow with the test_data/case01 and look at the results of the barcode03? It should be all of them 'Unclassified' and in barcode02 almost half of the sequences. If you don't see that, please update to the last version of the workflow.

Besides, you can use the flag --minimap2_by_reference to take a look on the minimap2 alignment results. Also, you can also take a look on the database to make sure the taxa you expected is included or your custom one to be sure of this.

Thank you very much!

nggvs commented 11 months ago

Hi @HannahBenisty , Have you checked the test data to see if you are able to see the unclassified sequences? If that is the case, could you close the issue if you consider the question has been already solved? Please, open any new issue to provide feedback or to report any issue that you find! Thank you very much for using the workflow!

HannahBenisty commented 10 months ago

Sorry, I did not have time to go back to this issue yet. I will close it and reopen in case I have time to do the test again. Many thanks for your help.