User: oconnwald

gravatar for oconnwald
oconnwald20
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20
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New User
Location:
Boulder, Colorado
Last seen:
6 days, 13 hours ago
Joined:
9 months, 2 weeks ago
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a*************@yahoo.com

Posts by oconnwald

<prev • 9 results • page 1 of 1 • next >
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Comment: C: bwa mem and multiply mapped reads
... Does anyone know where: > When a read matches in its entirety, with an equal score in multiple > locations, one of the locations is picked at random, is labeled as > primary, will be given a mapping quality of zero and will have an XA > tag that contains the alternative locations (this ...
written 6 weeks ago by oconnwald20
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Comment: C: Selecting Random Pairs From Fastq?
... What about: rand_records = random.sample(range(0, records), N) rand_records.sort() random.sample performs random selection without replacement, so the check you've added above would just be built-in to the call. ...
written 3 months ago by oconnwald20
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Comment: C: How does Base Call casing affect BWA
... 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 5 months ago by oconnwald20
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Comment: C: How does Base Call casing affect BWA
... 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 5 months ago by oconnwald20
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Comment: C: How does Base Call casing affect BWA
... 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 5 months ago by oconnwald20
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Comment: C: How does Base Call casing affect BWA
... 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 5 months ago by oconnwald20
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How does Base Call casing affect BWA
... 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) ...
alignment samtools bwa written 5 months ago by oconnwald20
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samtools mpileup -l gives the wrong REF base for some positions
... 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 ...
samtools mpileup written 7 months ago by oconnwald20
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Comment: C: Tools To Calculate Average Coverage For A Bam File?
... 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 9 months ago by oconnwald20

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