User: oconnwald
oconnwald • 20
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- Boulder, Colorado
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Posts by oconnwald
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... As an update, I've run the random-cased fastqs alignment with our reference modified to not include masking (i.e. I capitalized all lower-case bases), and I'm getting equivalent results as I did when I ran alignment of the fastqs with the reference with masking. So, I think the casing is here makin ...
written 10 days ago by
oconnwald • 20
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... That's interesting -- but the ordering of the reads isn't changing in each run (only casing), so I don't know if the first link applies. We are using a reference that has masked bases though. ...
written 11 days ago by
oconnwald • 20
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... Total reads includes supplemental reads -- you can see the offset on both is +12. If there were variation in the number of raw reads in the same, you'd see that reflected in the read1 and read2 counts ...
written 11 days ago by
oconnwald • 20
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... Just a simple Python script (I'm happy to post it if you'd like). I've confirmed that the random casing reads are identical in content (other than casing) by converting the random-cased bases back to the original upper casing and running a diff. ...
written 11 days ago by
oconnwald • 20
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... I was wondering how the casing of base calls affected BWA MEM performance.
I ran three sets of data to see if there was any difference at all:
- All base calls capitalized
- All base calls lower-cased
- Random casing for all base calls
I found that the first two sets (when casing was consistent) ...
written 11 days ago by
oconnwald • 20
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... When I use Samtools (v1.7 or v.1.10) mpileup with -l option to specify the positions I want, many REF bases are incorrect. When I use the -r command (in addition to -l), however, I get the correct bases.
For instance, I use these two commands to test consistency between using the -l vs -r options ...
written 10 weeks ago by
oconnwald • 20
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... You can install the executable from their github release page: https://github.com/brentp/mosdepth/releases
Latest version at time of commenting (0.2.9):
(Download executable)
`wget https://github.com/brentp/mosdepth/releases/download/v0.2.9/mosdepth`
(Update permissions to run it)
`chmod a+x m ...
written 4 months ago by
oconnwald • 20
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