Cross-species comparisons from different sequencing runs

[twhitney (Tabor)]

Hi there,

I am currently working on running samples from different species through QIIME2. Some of these samples were run on different sequencing runs and some were generated by both Illumina Miseq and Hiseq platforms. Unfortunately most of the data were acquired from public databases and not every paper publishes if it was run with a 33 or 64 PHRED score. I ran the first import with 33 and received the error message shown in the attached photo "Some of the PHRED quality values are out of range."

I ran these samples through deblur out of curiosity with a trim length of 100bp, and it worked while generating the expected filtering statistics we have from past data on this specific project and samples.

I am wondering if it is possible to run all these samples at the same time if they were sequenced on different platforms, or if I need to remove the species that are causing this error message before moving onto diversity and taxa analysis?

Attached is the demux.qsv output and file!

demux.qzv (296.4 KB) !

Thanks

[wasade (Daniel McDonald)]

Hi @twhitney,

Deblur does not utilize PHRED scores, and was designed specifically to integrate data from across different Illumina sequencing runs. So, no need to remove records where the PHRED offsets are incorrect.

Best,
Daniel

[twhitney (Tabor)]

Awesome, that is what we thought! Thank you!