User: -_-

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-_-860
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Posts by -_-

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Answer: A: How to plot RNASeq data in PCA
... I built an app to facilitate visualization of TCGA RNA-Seq data, may be helpful to your similar use cases, https://prettyomics.herokuapp.com/ ...
written 19 months ago by -_-860
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Comment: C: Where are mutation files (MAF) for TCGA normal samples on Firebrowse
... Not really. But I think the later is filtered is oncotator somehow ...
written 23 months ago by -_-860
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Comment: C: Where are mutation files (MAF) for TCGA normal samples on Firebrowse
... Not really. But I think the later is filtered is oncotator somehow ...
written 23 months ago by -_-860
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Comment: C: Where to get somatic mutations from WGS data?!
... I meant to ask if mutation for WGS (whoe-genome sequencing) data are available. I've only found that for WXS (whole-exome sequencing) data. From what I have read, seems it's not available. A related question is I wonder if whole-exome in the context of TCGA include 3' UTRs or not. ...
written 2.0 years ago by -_-860
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Comment: C: Does exome capture kit in TCGA project include UTR region
... Have you found the answer, please? ...
written 2.0 years ago by -_-860
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Comment: C: Finding miRNA motifs from Exome sequencing
... Any update on this? I also wonder if exome sequencing contains 3' UTR regions ...
written 2.0 years ago by -_-860
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Comment: C: Where to get somatic mutations from WGS data?!
... @Anthony Mathelier, could you please confirm if there is indeed no mutation calls (either in MAF or VCF) for WGS data? I really don't want to call them myself if possible as other people probably have done it already. ...
written 2.0 years ago by -_-860
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Comment: C: Exome and UTRs
... Any update on this? I am interested in mutation in 3' UTR regions. ...
written 2.0 years ago by -_-860
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Comment: C: Where are mutation files (MAF) for TCGA normal samples on Firebrowse
... I got it, it's in Sequence_Source column. But I found it's all WXS for 993 BRCA MAF files. Where could I find MAF for whole-genome sequencing data, please? ...
written 2.0 years ago by -_-860
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Comment: C: Where are mutation files (MAF) for TCGA normal samples on Firebrowse
... Thanks for the insight! Also, how could I know if they are called from genome or just exome data. I am mainly interested in mutations in non-coding regions. ...
written 2.0 years ago by -_-860

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