Plugin similar to fastx_quality_stats from FASTX-toolkit?

[A_Bennett (Alexa)]

I am searching for a plugin which can return quality data in a table format for a demultiplexed qza file. At a minimum, it should provide number of reads at a position, mean score, and quartiles.

I am currently having an issue where the subsampling is misrepresenting several of my data sets compared to a FASTX report or when viewed in FASTQC. I would rather my entire pipeline be within the QIIME2 environment for tracking purposes.

(Sorry for the duplicate submission. I accidently clicked Create Topic before completion.)

[SoilRotifer (Mike Robeson)]

Hi @A_Bennett,

@A_Bennett

I am searching for a plugin which can return quality data in a table format for a demultiplexed qza file. At a minimum, it should provide number of reads at a position, mean score, and quartiles.

I am not aware of a plugin that does this, though I am sure others on the forum might be able to come up with a neat trick or two?

@A_Bennett

I am currently having an issue where the subsampling is misrepresenting several of my data sets compared to a FASTX report of when viewed in FASTQC.

How so? Do keep in mind that you can alter the subsampling depth with qiime demux summarize by adding the --p-n flag as shown here.

Also, keep in mind that the FASTQC plot will be different, as it bins some of the positions unlike QIIME's built-in quality plots. For more details see:

FastQC compared to QIIME 2 quality plot

Okay, that is really helpful! First, your paired-end plot is based on 13 sequences (!!!), while your single-end plot is based on 555154.... So, that is a good first step in tracking down why the plots look so drastically different (the sample size for the box plots are orders of magnitude different). BTW, I pulled that information from the table on the first page of the viz near the top. Second, by looking through the provenance of the visualizations, I noted that you demuxed the single-end rea…

-Mike

[A_Bennett (Alexa)]

@SoilRotifer

How so?

The reverse reads have a large inner-quartile spread. The FASTX-Toolkit and QIIME2 (default settings) differ by up to 20 bases if using the threshold of mean quality below phred score of 30.

@SoilRotifer

Also, keep in mind that the FASTQC plot will be different, as it bins some of the positions unlike QIIME’s built-in quality plots. For more details see:

Nice refresher! Good thing I only used this as a quick visual tool after comparing the QIIME and FASTX outputs.