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Using bwa mem instead of bwa aln in 02-variant_calling.md #111

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taylorreiter opened this issue Jan 25, 2018 · 9 comments

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commented Jan 25, 2018

In datacarpentry/wrangling-genomics/_episodes/02-variant_calling.md, bwa aln is taught instead of bwa mem. I see the note about bwa mem, but I think most people who will be taking this work shop will be working with reads >50bp. I think teaching bwa mem instead of bwa aln > bwa samse will simplify the learning process & lesson time, and give the learners a better understanding of the pipeline they will probably use when they do alignment with their own data. Thoughts?

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commented Jan 25, 2018

+1

We did this last year at CSUMB. The SAI/SAM two-step is an extra step that the learners simply have to "trust us" is necessary. And unless they're going to be working with very short reads in the future, they're going to be using BWA MEM in the future anyway.

Note that to keep things consistent, it might be worth identifying/creating a new sample data set with 2x75 bp or 2x100 bp reads, for which BWA MEM would be indisputably the better choice.

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commented Jan 25, 2018

Rewrote for UC Davis Genomics workshop here:
https://github.com/taylorreiter/wrangling-genomics/blob/gh-pages/_episodes/02-variant_calling.md

This version took me 1.5 hours to teach. I covered samtools tview and mentioned IGV. I did not get to the challenge problems.

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commented Apr 13, 2018

Was this submitted as a PR? I'm getting this when I try to compare taylorreiter/wrangling-genomics to datacarpentry/wrangling-genomics.

screen shot 2018-04-13 at 9 55 03 am

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commented Apr 17, 2018

no...only #115 was merged. I'm confused why you got that page

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commented Jun 26, 2018

@fpsom is this an issue I can submit a PR for?

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commented Jun 27, 2018

@taylorreiter yes please!

@ErinBecker

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commented Oct 23, 2018

This change has been approved by the Curriculum Advisors. in conjunction with the transfer to a new data set. @taylorreiter.

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commented Feb 14, 2019

I think this issue has been resolved now! @ErinBecker @taylorreiter should we close the issue?

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commented Feb 14, 2019

Yes! Thanks for the ping @fpsom.

@ErinBecker ErinBecker closed this Feb 14, 2019

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