Moderator: Jeremy Leipzig
Jeremy Leipzig ♦ 17k
- Reputation:
- 16,670
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- Philadelphia, PA
- Website:
- http://jermdemo.blogsp...
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- jermdemo
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- Last seen:
- 2 hours ago
- Joined:
- 7 years, 5 months ago
- Email:
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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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... yes nice support for ontologies to define input/output formats in CWL
https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl/blob/master/tools/fastq_to_fasta.cwl
cwlVersion: v1.0
class: CommandLineTool
hints:
- class: SoftwareRequirement
packages:
biopytho ...
written 20 days ago by
Jeremy Leipzig ♦ 17k
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... ![http://i.imgur.com/IAYtE2il.png][1]
[1]: http://i.imgur.com/IAYtE2il.png ...
written 9 weeks 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 10 weeks ago by
Jeremy Leipzig ♦ 17k
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Comment:
C: is seqanswers.com down?
... https://twitter.com/SEQanswers/status/864165020669587456 ...
written 10 weeks 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 12 weeks ago by
Jeremy Leipzig ♦ 17k
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... see https://www.biostars.org/p/77840/ ...
written 3 months ago by
Jeremy Leipzig ♦ 17k
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... show us one that's missing ...
written 3 months 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 3 months 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 3 months 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 3 months ago by
Jeremy Leipzig ♦ 17k
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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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