User: senowinski

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senowinski10
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European Union
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1 month, 3 weeks ago
Joined:
2 years, 10 months ago
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Posts by senowinski

<prev • 16 results • page 1 of 2 • next >
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Comment: C: How to identify the important SNPs from several GWAS studies
... Yes @geek_y I am asking that exactly. While sometimes the SNP identified by GWAS may be in LD with the "real" SNP, I thought this could be circumvented by identifying those SNPs significantly associated with a disease by several studies? Whereas identifying how other SNPs are reliable, I could use t ...
written 8 weeks ago by senowinski10
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Answer: A: TCGA PRAD Data Germline BRCA1/2 status
... Solved - good news, you can still download normal tissue (blood/normal adjacent) WXS VCFs from current (not archived) repository and then annotate to obtain BRCA1/2 mutational status! ...
written 9 weeks ago by senowinski10
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How to identify the important SNPs from several GWAS studies
... When trying to pool all the SNPs identified as being associated with a disease from different GWAS studies. How do you determine which are actually of interest? Are there any other things (than the below) to look out for when determining whether or not SNPs found significantly associated to a diseas ...
snp written 9 weeks ago by senowinski10 • updated 9 weeks ago by vchris_ngs4.2k
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Comment: C: Combining fastq/sorted sam files from same libraries run on HiSeq and NextSeq
... I want to call copy number variations on them. I should also add, this is low-pass sequencing combined depth of coverage will be 0.2X. thanks ...
written 10 weeks ago by senowinski10
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Combining fastq/sorted sam files from same libraries run on HiSeq and NextSeq
... Can I combine fastq/sorted sam files from the same samples and same libraries that were run on both the HiSeq and NextSeq? If it is absolutely fine (are there any pitfalls?), is there anything I should be weary of? Thanks! ...
next-gen sequencing written 10 weeks ago by senowinski10 • updated 10 weeks ago by Devon Ryan73k
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what is the lowest coverage the human genome can be sequenced at to provide roughly the same resolution as SNP6?
... What depth of coverage of the human genome would roughly provide the same copy number resolution of SNP6? I want to know this so that I can calculate some kind of a b-allele-frequency at roughly the same frequency as SNP6? Where let's say there is a probe every ~0.00189Mb, would this mean a minimu ...
next-gen snp sequencing written 3 months ago by senowinski10 • updated 3 months ago by Brian Bushnell14k
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TCGA PRAD Data Germline BRCA1/2 status
... Hi, Does anyone know where I can get hold of Germline BRCA1/2 status of TCGA PRAD samples that has already been published? I no longer have access to the legacy VCFs (which I think may have germline information). Thanks! ...
sequencing written 5 months ago by senowinski10
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Comment: C: bwa mem not aligning
... Thank you for noticing I didn't properly go through my question! I have tried all possible combinations of read1 and 2 from lane 3 and 4 from this sample because it is not aligning. and all have the same outcome - skipped all 4 orientations. I have 28 samples that aligned well, but not the case for ...
written 8 months ago by senowinski10
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Comment: C: bwa mem not aligning
... I get this error from read1 and 2 from lane 3 and 4 of this sample. all my other samples were fine. so I also thought something similar - so I tried all alignment combinations of read1 and 2 from the different lanes with the same problem - I also tried concatenation read1s from lane 3 and 4 and alig ...
written 8 months ago by senowinski10
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Comment: C: bwa mem not aligning
... fastqc was fine - no flags. this is a problem with read 1 and read 2 from lane 3 and 4 of this sample. I have 29, and this is the only one with this problem ...
written 8 months ago by senowinski10

Latest awards to senowinski

Scholar 9 weeks ago, created an answer that has been accepted. For A: TCGA PRAD Data Germline BRCA1/2 status
Popular Question 8 months ago, created a question with more than 1,000 views. For Varscan 2 output
Popular Question 2.7 years ago, created a question with more than 1,000 views. For What absolute copy number would you call an Amplification?

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