User: MatthewP

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MatthewP120
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120
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China
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4 hours ago
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1 year ago
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Posts by MatthewP

<prev • 67 results • page 1 of 7 • next >
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Will many zero values of relative frequency cause LEFSe error?
... Hello, I need to run [LEFSe][1] after [Qiime2][2] pipeline. First I do follow steps to export relative frequency data and convert file format. Get genus(level 6 of [silver][3]) ralativate frequency and convert file format. # extract level 6 data qiime taxa collapse \ --i-table table ...
lefse qiime2 written 3 days ago by MatthewP120
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Comment: C: Script: VCF to 3 base mutation pattern
... What about `indel` data? Discard? ...
written 12 days ago by MatthewP120
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Comment: C: How to use result of CNVkit to estimate purity by PureCN
... Thanks @markus.riester. I tried to run a small test but some error raised. My code library(PureCN) normal_hdf5 <- "/MntWorkdir/GATK_CNV/P2_PBMC.hdf5" tumor_hdf5 <- "/MntWorkdir/GATK_CNV/P2_hdf5/P2-3.recal.hdf5" interval_file <- "/MntWorkdir/BGI_ex_region_hg19_preprocessed ...
written 12 days ago by MatthewP120
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Comment: C: Usage of Mutect2
... Maybe you should try [germline pipeline][1] which use [HaplotypeCaller][2] instead of `Mutect2` . [1]: https://software.broadinstitute.org/gatk/best-practices/workflow?id=11145 [2]: http://HaplotypeCaller ...
written 13 days ago by MatthewP120
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Answer: A: Usage of Mutect2
... Hello, `normal` here means normal tissue. People need to compare variants from tumor tissue and normal issue(example: [PBMC][1]) to find some variants new(somatic) in tumor tissue. [1]: https://en.wikipedia.org/wiki/Peripheral_blood_mononuclear_cell ...
written 14 days ago by MatthewP120
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Comment: C: How to use result of CNVkit to estimate purity by PureCN
... Hello, I want to use results from [gatk pipeline][1], do you have any ideas how to do in `PureCN`? I see no example in `PureCN` [overview][2] and [quickstart][3]. Thanks. [1]: https://software.broadinstitute.org/gatk/documentation/article?id=11683 [2]: https://bioconductor.org/packages/release ...
written 14 days ago by MatthewP120
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Comment: C: Any database can substitute OMIM?
... genes(mutations) and phenotype. ...
written 22 days ago by MatthewP120
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Any database can substitute OMIM?
... [OMIM][1] is good, but I need to download data freely. Any one knows any database like `omim`? [1]: https://www.omim.org/ ...
omim written 22 days ago by MatthewP120 • updated 20 days ago by Charles Warden6.9k
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How to draw heatmap plot use cnv seg data called by gatk?
... Hello, everyone. I follow this [tutorial][1] to call `CNV` for my `WES` data. After command `ModelSegments` we can get `seg` data and plot use `PlotModeledSegments` , this give `CNV` plot for each sample. I have many samples(100+) and want to generate a heatmap to see what's differentce(/common) bet ...
gatk cnv heatmap written 4 weeks ago by MatthewP120 • updated 29 days ago by Kevin Blighe44k
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Answer: A: How to get actual location of CNV from CNVKit
... Hello, use `cnvkit.py segment` command will give you segments `CNV` change, which shows the actual genomic coordinates. If you use `cnvkit` you better read this [tutorial][1]. [1]: https://cnvkit.readthedocs.io/en/stable/pipeline.html ...
written 4 weeks ago by MatthewP120

Latest awards to MatthewP

Scholar 5 months ago, created an answer that has been accepted. For A: How to convert data from NCBI E-utilities.efetch to python data object?
Supporter 5 months ago, voted at least 25 times.

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