User: moldach

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moldach120
Reputation:
120
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Trusted
Location:
McGill, Douglas Mental Health University Institute
Website:
https://medium.com/@Ma...
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MattOldach
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Last seen:
9 hours ago
Joined:
4 years, 2 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 • 40 results • page 1 of 4 • next >
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GCTA GREML for WGS with extremely large number of samples and SNPs
... I've been trying to use [GCTA (a tool for Genome-wide Complex Trait Analysis)][1] for a larger job than usual and keep getting a message saying "killed" from our cluster when trying to do the segment based LD score step on my data which makes me think it's a memory issue. We don't have a job schedul ...
genome greml gcta written 6 weeks ago by moldach120
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Probe filtering beta-values from rgSet
... I've see many NA's for beta-values in my rgSet object (either because some probe/CpGs were specifically set NA or because of transformation from intensities to beta-values). beta <- minfi::getBeta(rgSet) sum(is.na(beta)) # 16,928 I'm trying use the `DNAmArray` R packages `probeFiltering ...
R cpgs dnamarray minfi rgset written 6 weeks ago by moldach120
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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 4 months ago by moldach120
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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 6 months ago by moldach120
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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 6 months ago by moldach120
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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 6 months ago by moldach120
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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 7 months ago by moldach120
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Comment: C: compare two gene lists
... Sadly this does not work even on numerically sorted ASCII text files ...
written 14 months ago by moldach120
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Comment: C: compare two gene lists
... Indeed I did *facepalm*, edited the post to include it now ...
written 14 months ago by moldach120
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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 14 months ago by moldach120

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Popular Question 10 weeks ago, created a question with more than 1,000 views. For Problem Viewing Alignments in IGV When Loading Custom FASTA file
Popular Question 4 months ago, created a question with more than 1,000 views. For Problem Viewing Alignments in IGV When Loading Custom FASTA file
Popular Question 7 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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