User: moldach

gravatar for moldach
moldach130
Reputation:
130
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Location:
McGill, Douglas Mental Health University Institute
Website:
https://medium.com/@Ma...
Twitter:
MattOldach
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Google Scholar Page
Last seen:
1 month, 3 weeks ago
Joined:
5 years, 4 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 • 44 results • page 1 of 5 • next >
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Comment: C: ImportError: cannot import name zip_longest
... Oh shoot, I didn't catch that mistake. Thank you! ...
written 8 weeks ago by moldach130
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Comment: C: ImportError: cannot import name zip_longest
... Istavan, what you say about the use of `sudo` makes sense; indeed the [instructions for testing say *not to*](https://github.com/etal/cnvkit). This is why I'm unsure why I cannot *run make without the use of sudo*? (cnvkit) mtg@pop-os:/bin/cnvkit/test$ make python ../cnvkit.py import-picard ...
written 8 weeks ago by moldach130
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Comment: C: ImportError: cannot import name zip_longest
... Sorry about the confusion. I've edited the post to make it (*hopefully*) clearer. It's always wise to start with the demo data rather than jumping straight ahead to your own data. If you install via `conda` I'm not sure where the `cnvkit/test/` folder ends up. This is why I've also imported the cnv ...
written 8 weeks ago by moldach130
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Comment: C: ImportError: cannot import name zip_longest
... I'm having similar issues on POP!_OS (built off Ubuntu 19). I've made a conda environment that uses python3 but get the same error: ##Check versions of conda and python (base) mtg@pop-os:/bin/$ conda --version conda 4.8.3 (base) mtg@pop-os:/bin/cnvkit$ python3 --version Python 3.7. ...
written 8 weeks ago by moldach130
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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 16 months ago by moldach130
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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 16 months ago by moldach130
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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 18 months ago by moldach130
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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 21 months ago by moldach130
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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 21 months ago by moldach130
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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 21 months ago by moldach130

Latest awards to moldach

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 13 months ago, created a question with more than 1,000 views. For Problem Viewing Alignments in IGV When Loading Custom FASTA file
Popular Question 13 months ago, created a question with more than 1,000 views. For Looking for a Chromatin database
Popular Question 17 months ago, created a question with more than 1,000 views. For Problem Viewing Alignments in IGV When Loading Custom FASTA file
Popular Question 19 months ago, created a question with more than 1,000 views. For Problem Viewing Alignments in IGV When Loading Custom FASTA file
Popular Question 22 months ago, created a question with more than 1,000 views. For Problem Viewing Alignments in IGV When Loading Custom FASTA file
Autobiographer 2.7 years ago, has more than 80 characters in the information field of the user's profile.

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