User: robles.daniela

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A PhD student trying to learn about bioinformatics.

Posts by robles.daniela

<prev • 13 results • page 1 of 2 • next >
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Answer: A: GDC API query to map HT-seq FPKM UUID to a Case UUID
... Hi Matt, I've in fact just done this but with a different TCGA dataset (SKCM). What I did was download the JSON dump of all the cases in your dataset (which, if I have understood correctly, in your case should be here: https://portal.gdc.cancer.gov/repository?facetTab=files&filters=%7B%22op%22 ...
written 4 days ago by robles.daniela50
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Comment: A: Can I use TCGA FPKM-UQ values directly to compare across samples without any pre
... Thanks so much both! I had seen that chart, Kevin, that is why I thought I could use FPKM-UQ directly. But given your advice and the paper Cindy sent over I will use HTSeq-counts and process through DESeq2 before doing any analyses. I will then compare with the results from using FPKM-UQ directly an ...
written 10 days ago by robles.daniela50
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Comment: C: Can I use TCGA FPKM-UQ values directly to compare across samples without any pre
... Dear Kevin, thanks so much for your answer! This is really helpful. I have one remaining question, I would be grateful if you could help me: I thought the FPKM-UQ was a modification of the FPKM normalisation to precisely allow cross-sample comparison, is this not the case then? ...
written 10 days ago by robles.daniela50
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Can I use TCGA FPKM-UQ values directly to compare across samples without any preprocessing?
... Dear all, This is a newbie question :) I'm building a linear model to identify significant predictors of mutation count/types in tumours from TCGA. I want to include expression levels of a couple of genes, but I am quite new to RNA-Seq analyses and best practices. TCGA provides RNA-Seq data at the ...
fpkm-uq tcga rna-seq written 10 days ago by robles.daniela50
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Comment: C: Next-generation DNA sequencing: How to tell systematic errors from real SNVs?
... Thank you for your useful suggestion, Christian. I have activated all repeat tracks in the UCSC Genome Browser for this variant but none seem to overlap it... will keep looking for the solution. ...
written 2.2 years ago by robles.daniela50
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Comment: C: Next-generation DNA sequencing: How to tell systematic errors from real SNVs?
... Thanks very much for your suggestion Brian. I used a different caller (GATK HaplotypeCaller) and indeed it seems the variant is not being called. However I'm a bit puzzled as to why it is so common in the exac data if I suspect loads of those exomes used GATK. Maybe they used GATK UnifiedGenotyper, ...
written 2.2 years ago by robles.daniela50
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Next-generation DNA sequencing: How to tell systematic errors from real SNVs?
... Hi all, I hope you're well. I have one question regarding variant calling in NGS data. We have sequenced a number of human germline exomes, captured with Agilent SureSelect 50mb All Exon kit, in the Illumina GAII platform, paired-end, 75bp reads. We have aligned with BWA and called variants with S ...
alignment next-gen sequence snp sequencing written 2.2 years ago by robles.daniela50 • updated 2.2 years ago by Christian2.6k
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Comment: C: Samtools Pileup Format
... Yes, I see it now. Thanks for making everything clearer! ...
written 3.8 years ago by robles.daniela50
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Comment: C: Samtools Pileup Format
... Thanks very much Pierre. Than then settles it! :) ...
written 3.8 years ago by robles.daniela50
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Samtools Pileup Format
... Dear all, I hope you're well. I have a naive question about the samtools pileup format. The format looks like this: http://samtools.sourceforge.net/pileup.shtml My question is really what the 6th column is referring to. In that document (which is the official one), it says these are the base qual ...
quality samtools mpileup written 3.8 years ago by robles.daniela50 • updated 3.8 years ago by Devon Ryan73k

Latest awards to robles.daniela

Popular Question 2.2 years ago, created a question with more than 1,000 views. For Next-generation DNA sequencing: How to tell systematic errors from real SNVs?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Samtools Pileup Format
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Evaluating The Effect Of A Snp In A Tf Binding Site With The Ensembl Api
Student 4.6 years ago, asked a question with at least 3 up-votes. For Evaluating The Effect Of A Snp In A Tf Binding Site With The Ensembl Api

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