User: ernfrid

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ernfrid180
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6 months, 3 weeks ago
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Posts by ernfrid

<prev • 34 results • page 1 of 4 • next >
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Answer: A: what does "q2" mean in bam-readcount results?
... q2 in this case means bases with Phred quality score of 2. At the time bam-readcount was written, bases of this quality indicated an error in the read as determined by Illumina's software ( http://seqanswers.com/forums/showpost.php?p=17491&postcount=3). See the SomaticSniper paper (https://www.n ...
written 6 months ago by ernfrid180
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Answer: A: any option in somatic sniper to analyze on a region or bed file of regions?
... No, there is not. This other Biostars question and answer provide a work around. https://www.biostars.org/p/138551/ ...
written 11 months ago by ernfrid180
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Answer: A: bam-readcount fails to report all positions
... 1) If you'd prefer a stable release over the most recent code changes, you can checkout the v0.7.4 tag (`git checkout v0.7.4`) before following the build instructions. 2) Your command lines look correct to me. It's interesting that you see improvement when using bowtie. I have never used gsnap. Off ...
written 13 months ago by ernfrid180
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Answer: A: bam- readcount error
... This error indicates that bam-readcount's internal mechanisms for caching per-read statistics are failing and that is likely the reason your results are incorrect. This is due to a bug in calling bam-readcount without requesting a region. For your case, a decent workaround may be to just request the ...
written 16 months ago by ernfrid180
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Answer: A: speed of bam-read count is too slow
... `bam-readcount` generates many stats at a given position. As shown in the other two answers, if you are looking for general or simple readcounts then other strategies will be much faster. If you do want all the stats then one common cause of excessive `bam-readcount` slowness is if the sites you pro ...
written 18 months ago by ernfrid180
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Answer: A: all the SV type of breakdancer output are ITX is that correct?
... Breakdancer will call ITX if the read pairs are everted. Is this a standard Illumina library? I assume it most likely is, but mate-pair libraries are not supported with 1.4.5. Even with standard libraries, if the insert size is small the reads tend to get clipped and result in read pairs that show t ...
written 20 months ago by ernfrid180
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Comment: C: Problem to install Breakdancer on Mac OS X
... I never saw this update, but I did push a correction about a week ago that may fix your issue. Can you try it again? ...
written 23 months ago by ernfrid180
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Answer: A: Installing Joinx on Linux-x86_64
... Your lack of git is likely to be the issue. The versioning code all depends on utilizing git to grab tags from the repository. You should follow Ram's instructions and see if that fixes your problem. ...
written 23 months ago by ernfrid180
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Answer: A: Understanding flags from output of bam2cfg.pl - BreakDancer
... The supported version of breakdancer is now on github: https://github.com/genome/breakdancer That said, the flag values are not documented anywhere that I'm aware of. The below assume you are working with standard Illumina libraries and are BreakDancer's default interpretation. I've tried to create ...
written 2.2 years ago by ernfrid180
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Comment: C: Need help understanding read depth for somaticsniper vcf's
... I realize it's been about a year, which is sad. In the event that you are still interested, the latest version (1.0.5.0) should fix the bug(s) you discovered. ...
written 2.2 years ago by ernfrid180

Latest awards to ernfrid

Teacher 10 months ago, created an answer with at least 3 up-votes. For A: bam-readcount reports all reference bases as N
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: bam-readcount reports all reference bases as N
Scholar 3.4 years ago, created an answer that has been accepted. For A: bam-readcount reports all reference bases as N
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: bam-readcount reports all reference bases as N

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