User: harold.smith.tarheel

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Posts by harold.smith.tarheel

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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 6 days ago by harold.smith.tarheel3.8k
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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 14 days ago by harold.smith.tarheel3.8k
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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 14 days ago by harold.smith.tarheel3.8k
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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 14 days ago by harold.smith.tarheel3.8k • updated 14 days ago by andrew.j.skelton733.7k
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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 16 days ago by harold.smith.tarheel3.8k
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Answer: A: How to do a local denovo assembly including unmapped paired reads for many sampl
... If you know the exact sequence and location of the insertion, and you just need to confirm presence/absence, what not 'grep' the FASTQs for the genome/insert junction sequences? Or am I missing something? ...
written 28 days ago by harold.smith.tarheel3.8k
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Answer: A: Finding of origin of replication in a bacterial Genome
... Computationally? There's [Ori-Finder][1]. [1]: http://tubic.tju.edu.cn/Ori-Finder/ ...
written 6 weeks ago by harold.smith.tarheel3.8k
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Answer: A: Differentiating between chromosomal and plasmid DNA
... 1) From WGS data, chromosome vs episome can be distinguished by copy number (reflected in differences in read depth). With appropriate data, you can also assemble the genomes and distinguish the two by contigs. 2) Search for 'amplicon sequencing'. Note that the MiSeq, at 10M+ reads/run, is overkill ...
written 7 weeks ago by harold.smith.tarheel3.8k
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Answer: A: Get one maximum UTR per gene
... You could try [BEDTools 'merge'][1] to collapse overlapping UTRs into one, but I anticipate a few problems: 1) if any of the UTRs do not overlap, you'll still be left with multiples; 2) UTRs from different genes might overlap, and those would collapse as well. [1]: http://bedtools.readthedocs.io ...
written 8 weeks ago by harold.smith.tarheel3.8k

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