User: mtkk94

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mtkk9410
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2 years, 7 months ago
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Posts by mtkk94

<prev • 5 results • page 1 of 1 • next >
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gCNVKERNEL Error while using GATK 4.1
... Hi, I am trying to run GATK 4.1 on WES data for germline CNV detection, and received an error about gcnvkernel. The error states that we do not have gcnvkernel installed, and we can not figure out how to install it. We have used the command "source activate gatk". We are using Python version 3.6.2. ...
gatk gcnvkernel cnv written 12 months ago by mtkk9410
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Error while using TCGAanalyze_DMR for >2 groups
... Hello, I'm trying to use TCGAanalyze_DMR for 2 groups (Indolent vs Aggressive). I have the below error. https://user-images.githubusercontent.com/41593805/45496569-5f9edb80-b73b-11e8-8484-51ce3a2e01a3.png What could be the reason for this error? Is it cause some of the values are NAs? but it save ...
tcgabiolinks R gleason score methylation written 20 months ago by mtkk9410
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Comment: C: How to download triple negative breast cancer RNA-seq fpkm data from GDC.
... Thank you for the solution. I've downloaded the clinical file and it's been difficult to map the IDs from clinical to that of expression matrix. Fortunately, I know how to code and mapped them back. Also, the clinical file I've obtained doesn't have any information regarding to control/normal sample ...
written 2.2 years ago by mtkk9410
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Answer: A: XHMM and PLINK/Seq problem
... "./sources/scripts/interval_list_to_pseq_reg This is present in XHMM and not in plink. Try finding it in "XHMM/sources/scripts/interval_list_to_pseq_reg" XHMM folder. ...
written 2.3 years ago by mtkk9410
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How to download triple negative breast cancer RNA-seq fpkm data from GDC.
... Hello, This might be a silly question but I couldn't find a tag to select triple negative breast cancer samples in GDC. I've tried downloading metadata of RNA-seq files and also clinical metadata but couldn't find a tag. I've also downloaded a single clinical file and tried searching for a tag but n ...
rna-seq sequencing written 2.6 years ago by mtkk9410

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Popular Question 2.1 years ago, created a question with more than 1,000 views. For How to download triple negative breast cancer RNA-seq fpkm data from GDC.

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