User: moldach

gravatar for moldach
moldach80
Reputation:
80
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Trusted
Location:
McGill, Douglas Mental Health University Institute
Website:
https://medium.com/@Ma...
Twitter:
MattOldach
Scholar ID:
Google Scholar Page
Last seen:
9 hours ago
Joined:
3 years, 9 months ago
Email:
m******@ucalgary.ca

Data-scientist/Bioinformatician working with various ‘Omics data (bulk RNA-seq, scRNA-seq, ATAC-Seq, ChIP-seq, Proteomics, GWAS). Comfortable using Linux, HPCs, Cloud-computing, Git, R programming and Python

Posts by moldach

<prev • 37 results • page 1 of 4 • next >
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Comment: C: PLINK heterozygosity - Negative F statistic?
... Thank you for that detailed response. It makes sense that those samples suffering from contamination are dropping out in other (upstream) steps of the QC pipeline. Furthermore, certain things we do in bioinformatics analysis can often be subjective in the sense that they are practices carried ov ...
written 7 weeks ago by moldach80
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Comment: C: PLINK heterozygosity - Negative F statistic?
... According to [this link][1]: "**The estimate of F can sometimes be negative. Often this will just reflect random sampling error, but a result that is strongly negative (i.e. an individual has fewer homozygotes than one would expect by chance at the genome-wide level) can reflect other factors, e.g. ...
written 8 weeks ago by moldach80
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Comment: C: PLINK heterozygosity - Negative F statistic?
... Excellent point Ram, I've added it as a comment now and apologize for posting as an answer originally - it was not. I feel your answer could be enriched by expanding upon what you meant when you say "negligible". Could you please, in a more objective way, define what that means? (*e.g.* providing ...
written 8 weeks ago by moldach80
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Comment: C: PLINK heterozygosity - Negative F statistic?
... I believe this adds to the top-level question by seeking greater clarity on what @Caragh asked: "*how much heterozygosity is too much heterozygosity? Is there a threshold that would indicate sample contamination or is it solely based on the distribution amongst the 48 [**n**] samples?* ...
written 8 weeks ago by moldach80
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Comment: C: compare two gene lists
... Sadly this does not work even on numerically sorted ASCII text files ...
written 9 months ago by moldach80
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Comment: C: compare two gene lists
... Indeed I did *facepalm*, edited the post to include it now ...
written 9 months ago by moldach80
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Comment: A: compare two gene lists
... I'm having a similar issue, albeit a more complex example, and have an ongoing question on Stack Overflow where `grep -h -w -f file2 file1` should work but for unknown reasons is not working. I would appreciate it if someone could take a [look at this][1] and suggest a solution. [1]: https://sta ...
written 9 months ago by moldach80
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Answer: A: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 201
... Ever since CRISPR-Cas9 was used to edit human cells in 2013 there has been optimism of treating virtually every disease. In 2018 we will likely see a move into the clinic [in Europe][1] and perhaps by 2019 in the U.S. There are [already trials in China][2] but researchers have yet to publish any ear ...
written 10 months ago by moldach80
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Comment: C: Handbooks for Bioinformatics Ninjas
... Inkscape is an awesome free-source alternative to Adobe Illustrator whereas GIMP is a free-source alternative to Adobe Photoshop. Both are good tools depending on what your ultimate aim is. GIMP/Photoshop are raster/bitmap graphics and are often used to edit photographs by adding effects and making ...
written 10 months ago by moldach80
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Answer: A: Is There A Database Of Known Dna Binding Proteins?
... [DNABP][1] is a database/manuscript, from late 2016, that built a machine learning method (Random Forest) to identify de-novo DNA-binding proteins using only sequence information: 1) the conservation of physiochemical protperties of the amino acids, and 2) the binding propensity of DNA-binding resid ...
written 10 months ago by moldach80

Latest awards to moldach

Popular Question 9 weeks ago, created a question with more than 1,000 views. For Problem Viewing Alignments in IGV When Loading Custom FASTA file
Autobiographer 13 months ago, has more than 80 characters in the information field of the user's profile.

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