User: susibing

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susibing20
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Posts by susibing

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Annotation of ID from TCGA gene expression data
... I have the following problem after converting the ensemble gene ids to HUGO symbols using the biomart package: When intergrating DNA seq and RNA seq data, HUGO symbols are only overlapping by ~75%; for instance the gene symbol ALPG (converted from RNA seq) is annotated as ALPPL2 in the DNA seq dat ...
written 13 months ago by susibing20
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Answer: A: bedtools multicov - tab-delimited bam files?
... Thanks! It was indeed the gff input file that was not tab-delimited.. Thank you very much. (Feeling kind of stupid now..) ...
written 23 months ago by susibing20
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bedtools multicov - tab-delimited bam files?
... Dear all, I am trying to use bedtools multicov using six bam files as input and a gff file to compare with and unfortunately receive the error message: "It looks as though you have less than 3 columns at line: 1. Are you sure your files are tab-delimited?" Does anyone know how to find out whethe ...
bedtools tab-delimited multicov error message written 23 months ago by susibing20
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Answer: A: TCGA germline and somatic snvs
... Just as an additional: after being in contact with the NCI GDC support, turns out that germline snvs are hidden in the aggregated-somatic_mutation files that are with closed access, just not annotated as germline. I was told to overlap the open access and controlled access files to retrieve the germ ...
written 23 months ago by susibing20
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Comment: C: TCGA: How to tell if the data is exome or WGS?
... As far as I can see, this column is not filled out in files from the harmonized portal. Does anybody has any idea why this is the case? And how I can find out about whether the variants are from WXS or WGS? ...
written 23 months ago by susibing20
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Comment: C: TCGA germline and somatic snvs
... Thank you very much! ...
written 2.1 years ago by susibing20
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Comment: C: TCGA genotype data
... Dear kelly.wang135, I am sorry for the late request for clarification - you did indeed find germline mutations in the vcf file from the harmonzied portal? As far as I understood, all germline mutations are already filtered out in the vcf files, no? In case I have overseen something, please let me ...
written 2.1 years ago by susibing20
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TCGA germline and somatic snvs
... Dear all, I am looking for already called and annotated germline and somatic snvs from different TCGA projects and have already been approved through dbGaP for the data access. Unfortunately, it seems that in the harmonized data portal during variant calling all germline mutations are already fil ...
harmonized legacy tcga snv sequencing written 2.1 years ago by susibing20

Latest awards to susibing

Popular Question 13 months ago, created a question with more than 1,000 views. For TCGA germline and somatic snvs
Scholar 23 months ago, created an answer that has been accepted. For A: bedtools multicov - tab-delimited bam files?

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