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New workshop data set #42

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standage opened this issue Apr 16, 2018 · 4 comments

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commented Apr 16, 2018

Thread datacarpentry/wrangling-genomics#111 brings up the concern that bwa aln is not appropriate for data the vast majority of our learners will be working with in their own research. In a similar vein, the data set itself is comprised of 1x35bp single-end reads. I propose that this module is updated with more recent data.

Here is an example: SRA accession SRR2584858. These are 2x101bp paired-end reads sequenced from E. coli with the HiSeq 2000 platform and published in 2016. Using the same reference genome as before, this particular data set results in 4 SNV calls and a single INDEL call from the variant calling workflow.

Note, I haven't checked this data for poly-N content, which is an important consideration given its relevance to the file search and redirection sections in the shell-genomics module.

@taylorreiter

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commented Jun 29, 2018

@JasonJWilliamsNY

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commented Jul 3, 2018

This would be a nice update. Needs to be coordinated at the level of the curriculum committee.

@raynamharris

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commented Jul 3, 2018

See this issue for a detailed description of new clean and messy spreadsheets, including a list of all the changes made to make the data messy, which could be added to the instructor notes or to the solution of a challenge.

https://github.com/data-lessons/organization-genomics/issues/1

@ErinBecker

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commented Mar 18, 2019

@ErinBecker ErinBecker closed this Mar 18, 2019

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