Moderator: Jeremy Leipzig
Jeremy Leipzig ♦ 17k
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- Philadelphia, PA
- Website:
- http://jermdemo.blogsp...
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- jermdemo
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- Last seen:
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- Joined:
- 7 years, 3 months ago
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I am a bioinformatics software developer known mostly for my posts on big-ass servers, damn microarray papers, and the reproducible research guilt trip, as well as my review of pipeline frameworks. I have worked in virology, crop genomics, and on various pediatric diseases as a programmer, analyst, and architect. I'm currently a PhD student at Drexel.
Posts by Jeremy Leipzig
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... ![http://i.imgur.com/IAYtE2il.png][1]
[1]: http://i.imgur.com/IAYtE2il.png ...
written 19 days ago by
Jeremy Leipzig ♦ 17k
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Comment:
C: is seqanswers.com down?
... Hello mjp!
We believe that this post does not fit the main topic of this site.
off-topic
For this reason we have closed your question. This allows us to keep the site focused
on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to ...
written 23 days ago by
Jeremy Leipzig ♦ 17k
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105
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Comment:
C: is seqanswers.com down?
... https://twitter.com/SEQanswers/status/864165020669587456 ...
written 23 days ago by
Jeremy Leipzig ♦ 17k
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... The problem is likely naming related (M vs MT) but the bigger issue is that this GATK realignment approach is really overkill for mitochondria sequences. You could easily do a real alignment using BLAST or something else more sensitive. There are no mitochondrial gold standard indels in your referen ...
written 5 weeks ago by
Jeremy Leipzig ♦ 17k
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... see https://www.biostars.org/p/77840/ ...
written 8 weeks ago by
Jeremy Leipzig ♦ 17k
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158
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... show us one that's missing ...
written 9 weeks ago by
Jeremy Leipzig ♦ 17k
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... Which sequencing labs have the highest standards in terms of providing wet lab protocols and bioinformatic metadata?
This is our wishlist of sequence metadata - we wouldn't expect all this but more than a sequence file on a thumb drive:
adapter_name
adapter_sequence
aliquots
...
written 9 weeks ago by
Jeremy Leipzig ♦ 17k
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... I take it you have aligned your sequences to rCRS and you have a .bam file? You can submit that to Haplogrep. You can also call the consensus sequence using samtools, which will yield a fasta you can submit to Mitomaster.
https://www.biostars.org/p/178510/
...
written 9 weeks ago by
Jeremy Leipzig ♦ 17k
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... Yes, the most useful questions on SE tend to be off-topic and under threat by the rigid Asperger people who run those sites. ...
written 9 weeks ago by
Jeremy Leipzig ♦ 17k
1
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323
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1
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Comment:
C: GWAS & Logistic regression in R
... It's probably still ok to use GAPIT for this, you just have to round the responses to 0 or 1, assuming these responses are ordered in some meaningful way ...
written 3 months ago by
Jeremy Leipzig ♦ 17k
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For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
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For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
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For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
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For Are There Websites Which Allow Users To Post Comments On Peer-Reviewed Articles?
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For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
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For Is There A Convention For Representing Indels In Diploid Genome Sequences?
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For Is There A Convention For Representing Indels In Diploid Genome Sequences?
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For Why Do Genbank And Refseq Have Different Coordinates For Mitochondrial Features?
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For A: How Much Does It Cost To Align A Flowcell In The Cloud?
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For A: Retrieve mutation position and ID for a mutation in hgvs format
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For A: How Much Does It Cost To Align A Flowcell In The Cloud?
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For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
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