User: moldach

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moldach110
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Location:
McGill, Douglas Mental Health University Institute
Website:
https://medium.com/@Ma...
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MattOldach
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Last seen:
12 hours ago
Joined:
4 years 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 • 38 results • page 1 of 4 • next >
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Where To Get The Genetic Map For The Haplotype Reference Consortium to phase the data externally using SHAPEIT software with family information
... The [Sanger Imputation Service][1] does not offer a pipeline that utilizes the family information during phasing. Therefore, [our pipeline][3] (previously) has been to previously use genetic maps from the 1000 Genomes (Phase 3) to phase the data externally using [SHAPEIT][2] software with family in ...
genome gwas shapeit phasing hrc written 8 weeks ago by moldach110
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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 4 months ago by moldach110
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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 4 months ago by moldach110
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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 4 months ago by moldach110
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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 4 months ago by moldach110
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Comment: C: compare two gene lists
... Sadly this does not work even on numerically sorted ASCII text files ...
written 12 months ago by moldach110
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Comment: C: compare two gene lists
... Indeed I did *facepalm*, edited the post to include it now ...
written 12 months ago by moldach110
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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 12 months ago by moldach110
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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 13 months ago by moldach110
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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 13 months ago by moldach110

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Popular Question 7 days ago, created a question with more than 1,000 views. For Problem Viewing Alignments in IGV When Loading Custom FASTA file
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Popular Question 5 months ago, created a question with more than 1,000 views. For Problem Viewing Alignments in IGV When Loading Custom FASTA file
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