Question: DNA-seq and RNA-seq bam from TCGA for a single sample
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gravatar for subhajit06
2.5 years ago by
subhajit06110
United States
subhajit06110 wrote:

Hello all, I am trying to find DNA-seq bam file and RNA-seq bam file from one sample. I also need vcf file for SNV callset. I am looking for some examples from TCGA data. It would be great if anyone could point out a paper that use dataset of this kind. Thanks for your help, --Subhajit

bam rna-seq one sample dna-seq • 1.1k views
ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by subhajit06110
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gravatar for mforde84
2.5 years ago by
mforde841.2k
mforde841.2k wrote:

Genomic data commons: https://gdc.cancer.gov/

But you won't be able to get the bam or germline variant calls unless you have dbGap approval. Regardless all the other level 3 data is available for public download. Also bioconductor has a good package called TCGAbiolinks.

ADD COMMENTlink written 2.5 years ago by mforde841.2k
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gravatar for subhajit06
2.5 years ago by
subhajit06110
United States
subhajit06110 wrote:

Thanks for your answer. We do have controlled data access. I am using GDC with the token to get level 1/2 data.

I wanna know, if anyone knows about a good data set (a set of samples) with both DNA-seq and RNA-seq bam files and vcf file with snv call.

ADD COMMENTlink written 2.5 years ago by subhajit06110

In GDC you can filter for both DNAseq and RNAseq, download the sample metadata, and match for sample id. Just be careful mixing and matching tissue types, also make sure to assess batch effects.

ADD REPLYlink written 2.5 years ago by mforde841.2k
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gravatar for subhajit06
2.5 years ago by
subhajit06110
United States
subhajit06110 wrote:

Thank you !! I will try that and let you know. Thanks for your helpful comment !

ADD COMMENTlink written 2.5 years ago by subhajit06110
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