Indrani Datta
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Recent activity by Indrani Datta Sort by recent activity-
Thank you for your reply. The interval list is comparable to the library which was profiled with the samples. Best.
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I did ran GATK depthofcoverage on these sample/normal. sample_id,total,mean,granular_third_quartile,granular_median,granular_first_quartile,%_bases_above_15TUMOR,4090171663,13.95,9,1,1,21.0 sample_...
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1. There is not a lot difference in read coverage between sample and normal. 2. I ran several other samples and they have similar hyper segmentation. This is how one of the normal plot looks like...
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I created a panel of Normals with couple of matched Normals from the cohort and ran one sample with this panel of Normals. The hyper segmentation didn't resolve with this panel of Normals either. T...
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Thanks. I will look into IGV installation then and reply back here.
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The mean log2 copy ratio is -3.080777967. I didn't turn on any GC correction while running GATK, do you mean any other steps we need to do GC correction. Thanks.
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Thanks for your reply again. When you say the magnitude of the difference ,do you mean the difference between mean log2 copy ratio between sample and its normal. Is there any direct email you could...
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Thank you for your reply. I just checked the denoised copy ratio mean and it is negative. Please suggest if any other corrections needed for model segment call.
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Q20 is slightly higher in matched normal than tumor. This is not a clinical sample though. Thanks
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No, I don't have panel of Normals. I used matched normal. And I looked into standarizedMAD.txt file, it is 0.3, does this look fine? Thanks.