Output the fate of reads

Hi,

I am running ‘Deblur’ with Qiime2. Everything ran well but I find Deblur discarded lots of reads during preprocessing. Here is my case: I have multiple samples with around 20000 reads for each. After running Deblur, only less than 1000 reads were retained in each sample. I am really confused why so many reads were discarded by Deblur?

BTW, there is a special demand for me to know which reads go to which ASV. I am wondering if there is a way to find out this information?

Thanks in advance,

Pengfan

Hi @Pengfan,

If you run deblur workflow directly, you can specify --keep-tmp-files, and the full detail should be in the contained log files. If there are a lot of singletons in the data, then those will drop out as (by default) the minimum abundance is 2 (see --p-min-size)

Best,
Daniel

…I’m not aware of a way to get access to this information directly from QIIME 2 right now though.

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