User: cindyz

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cindyz30
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2 years, 8 months ago
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2 years, 11 months ago
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Posts by cindyz

<prev • 4 results • page 1 of 1 • next >
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TCGA download using gdc client: unable to connect to API error
... Hi everyone, When I tried to download some TCGA bam files using gdc data transfer tool, i.e. ./gdc-client download 00c0f995-1429-4c2d-9ffd-dbb71ffeaba7 -t token/sometoken.txt I got the following error: 2017-07-20 09:33:16,230: ERROR: Unable to download 00c0f995-1429-4c2d-9ffd-dbb71ffeaba7: Unabl ...
gdc-client tcga written 2.7 years ago by cindyz30
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Comment: C: hg19 transcript mapping or exon overlap
... Do you mean you want to identify all exons of a transcript? If so you can use ucsc table browser (go to ucsc website -> tools -> table browser -> select clade: mammal; genome: human; assembly: hg19; group: genes and gene predictions; leave track and table as default -> either download ge ...
written 2.8 years ago by cindyz30
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Comment: C: Deseq2/Dexseq: why is LRT significant if estimated coefficients under two condit
... I guess testing for whether the full model fits better is in general different from assessing whether fold change is different from 1 but, under what conditions would fold change be close to 1 but the full model still fits significantly better? Also how can I visualize model fit in dexseq? ...
written 3.0 years ago by cindyz30
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Deseq2/Dexseq: why is LRT significant if estimated coefficients under two conditions are almost the same?
... Hi everyone, I have been using dexseq to perform differential exon usage analysis under 2 conditions (3 samples each) but some of the results seem confusing to me. (I am including deseq2 in the title because from my understanding dexseq and deseq2 use very similar methods except deseq2 does differe ...
dexseq R deseq2 rna-seq written 3.0 years ago by cindyz30

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