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add seven-number summary of read length distribution to summarize #71

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gregcaporaso opened this issue Nov 30, 2017 · 4 comments
Closed

add seven-number summary of read length distribution to summarize #71

gregcaporaso opened this issue Nov 30, 2017 · 4 comments
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@gregcaporaso
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@gregcaporaso gregcaporaso commented Nov 30, 2017

This is useful after read joining, as the reads will differ in length, and this information is essential to have for setting the trim length parameter for deblur denoise-*.

If you need convincing of why we should add this, check out how awful the Viewing summary of joined data with read quality section of the read joining community tutorial has to be without it.

@gregcaporaso
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@gregcaporaso gregcaporaso commented Dec 7, 2017

While making this change, let's also add the number of samples (maybe in the same table). I had to copy/paste the seqs/sample counts data into a text file to figure out the number of samples in one of these artifacts to track down an issue I was having with an analysis.

@gregcaporaso gregcaporaso self-assigned this Jan 17, 2018
@thermokarst thermokarst added this to Incoming in 2018.4 Feb 28, 2018
@ebolyen ebolyen moved this from Incoming to Week 3/12 in 2018.4 Feb 28, 2018
@ebolyen ebolyen moved this from Week 3/12 to Week 4/2 in 2018.4 Feb 28, 2018
@thermokarst thermokarst self-assigned this Mar 12, 2018
@ebolyen ebolyen moved this from Week 4/2 to In Analysis in 2018.4 Mar 12, 2018
@thermokarst thermokarst removed their assignment Mar 13, 2018
@thermokarst thermokarst moved this from In Analysis to Backlog (Automated) in 2018.4 Mar 13, 2018
@thermokarst thermokarst removed this from Backlog (Automated) in 2018.4 May 1, 2018
@thermokarst thermokarst added this to Backlog (Automated) in 2018.6 via automation May 1, 2018
@jakereps jakereps mentioned this issue Jun 8, 2018
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2018.6 automation moved this from Backlog (Automated) to Completed Jun 20, 2018
@julibeg
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@julibeg julibeg commented Mar 16, 2021

As far as I can tell, the current version of the read-joining tutorial still describes the old plot and does not mention the seven-number summary. It also notes "We plan to simplify this process in the near future." referencing this issue. I guess it has not been updated yet.

@andrewsanchez
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@andrewsanchez andrewsanchez commented Mar 17, 2021

Hi, @julibeg! The 7-number summary is on the interactive quality plot tab of the visualization output by qiime demux summarize. But you are correct, this tutorial needs to be updated. Thanks for the report! I created a new issue in the qiime2/docs repo (qiime2/docs#503). Would you be interested in submitting a pull request to update this section of the tutorial?

@julibeg
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@julibeg julibeg commented Mar 18, 2021

I just started using qiime. Thus, I guess it's better if more experienced users handle the tutorials.

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