User: andrew.j.skelton73

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Posts by andrew.j.skelton73

<prev • 620 results • page 1 of 62 • next >
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Answer: A: QTL /linkage trait mapping
... I highly recommend [matrixEQTL and the associated paper][1] [1]: http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/ ...
written 1 day ago by andrew.j.skelton734.3k
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Comment: C: BioVM - a virtual machine for Bioinformatics
... https://twitter.com/lpachter/status/937055346987712512?lang=en :) ...
written 2 days ago by andrew.j.skelton734.3k
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Comment: C: Base Recabiliration Filters out 88% of the reads
... This is from an RNA Seq experiment right, and you're attempting to call variants? AFAIK, `SplitNCigarReads` corrects the CIGAR string when reads span splice junctions, and forces filters for `MalformedReadFilter` and `ReassignOneMappingQualityFilter`, of which all of your reads seems to have passed. ...
written 7 days ago by andrew.j.skelton734.3k
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Answer: A: Cufflinks and StringTie
... use [bedtools][1] [1]: https://www.biostars.org/p/13516/ ...
written 7 days ago by andrew.j.skelton734.3k
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Comment: C: diffrential expression analysis
... It's in the Limma Users Guide (Hint: [look at page 101][1]). Try to be more specific with your questions, generally asking for tutorials and commands to blindly run isn't the best way to learn how or why you're doing something. [1]: https://www.bioconductor.org/packages/3.7/bioc/vignettes/limma ...
written 15 days ago by andrew.j.skelton734.3k
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Comment: C: Getting files from BaseMount (Using find command to loop through the symlinks)
... When using basemount, it works no problem for me to retrieve fastq. AFAIK, basemount isn't (or shouldn't be symlinking), the files should appear normally, but are only fully retrieved from base space when a command is carried out on them. I wonder if invoking the `-L` flag in find is treating them a ...
written 16 days ago by andrew.j.skelton734.3k
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Answer: A: Getting files from BaseMount (Using find command to loop through the symlinks)
... cp `find ./ -type f -name "*.fastq.gz"` ~/My_Fastq ...
written 16 days ago by andrew.j.skelton734.3k
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Answer: A: Using gVCF mode in HaplotypeCaller ( GATK4)
... You can run Joint genotyping on as little as 2 samples (ASAIK - If anyone has a link to contradict me, please share!), however it's the variant filtering stage that you may have trouble with. [In the GATK forums it's recommended that to use VQSR, at least 30 whole exome samples or 1 whole genome sam ...
written 20 days ago by andrew.j.skelton734.3k
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Answer: A: opensource grafical user interface for filtering millions of annotated variant
... [I asked a similar question and compiled a list in another post][1] - I updated it not long ago, so it's pretty current. [1]: https://www.biostars.org/p/194938/ ...
written 21 days ago by andrew.j.skelton734.3k
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Comment: C: WES -- How come I found 40% mutations intron regions
... You don't have to re-do the processing from MuTect2, but use GATK's [SelectVariants][1] to filter through your call set. [1]: https://software.broadinstitute.org/gatk/gatkdocs/3.7-0/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php ...
written 9 weeks ago by andrew.j.skelton734.3k

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