User: harold.smith.tarheel

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Posts by harold.smith.tarheel

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Answer: A: Why "Motile sperm domain-containing protein 2" has nothing to do with "sperm"?
... [Not really a bioinformatics question, but since I know the answer, here goes] MSP (major sperm protein) was first identified in nematode sperm. It forms filaments that drive sperm motility (crawling, not swimming). The MSP domain is evolutionarily conserved in a variety of transmembrane proteins i ...
written 5 days ago by harold.smith.tarheel3.9k
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Comment: C: mpileup for creating a consensus sequence
... For starters, you're using an old/deprecated version (v0.1.19) that did not include the BCFtools 'call' command (I believe it was 'view' back then). Update to the [current version][1] and try again. [1]: http://samtools.github.io ...
written 4 weeks ago by harold.smith.tarheel3.9k
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Answer: A: Nucleotide coverage if >5 reads
... You can use [BEDtools genomecov][1] command: bedtools genomecov -ibam FILE.BAM -d | awk '$4 > 4' | wc -l Divide the output by the size of the genome to get the percentage. [1]: http://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html ...
written 5 weeks ago by harold.smith.tarheel3.9k
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Answer: A: Is there any disease mainly caused by underexpression or overexpression of some
... Any of the cytologically detectable deletions or duplications that are dominant disease markers (such as trisomy 21, mentioned by @Asaf) are presumed to decrease/increase gene expression levels. Haplo-insufficient genes produce disease when one of the two copies is absent (e.g., Williams syndrome o ...
written 5 weeks ago by harold.smith.tarheel3.9k
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Answer: A: Convert SNPs from GrCh38 to 37
... Use NCBI's [remap][1] or UCSC's [LiftOver][2]. [1]: https://www.ncbi.nlm.nih.gov/genome/tools/remap [2]: https://genome.ucsc.edu/cgi-bin/hgLiftOver ...
written 10 weeks ago by harold.smith.tarheel3.9k
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Comment: C: retrospective trio analysis from WGS SNPs
... Thanks, Andrew. I'm using VCFtools for other metrics, so I'll probably test it first. Will report back with results. ...
written 11 weeks ago by harold.smith.tarheel3.9k
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Comment: C: retrospective trio analysis from WGS SNPs
... Thanks, Fabio. I'll check out Mendel and report back with results if I use it. ...
written 11 weeks ago by harold.smith.tarheel3.9k
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retrospective trio analysis from WGS SNPs
... We'd like to perform trio analysis of mice to detect de novo mutations (via WGS and variant calling). The complication: our mouse facility performs breeding in bulk (~15 each males and females). Mom-pup pairs are obviously straightforward. To identify dads, our strategy is to sequence all of the mal ...
trio lineage pedigree variant snp written 11 weeks ago by harold.smith.tarheel3.9k • updated 11 weeks ago by andrew.j.skelton734.1k
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How to calculate genetic diversity in inbred population
... It's been a few years (decades) since my last class in population genetics, so I require guidance. We have WGS from 16 individuals of an inbred mouse line and have performed joint variant calling with the GATK pipeline. We would like to determine the degree of genetic diversity in the strain, with a ...
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Comment: C: NanoDrop vs Bioanalyzer
... Try posting on the [SEQanswers][1] forum. [1]: http://seqanswers.com ...
written 11 weeks ago by harold.smith.tarheel3.9k

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Scholar 3 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Scholar 3 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
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Scholar 5 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
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