Question: No CNV calls in CNVkit import-rna
0
gravatar for a.v.vliet
22 months ago by
a.v.vliet0
a.v.vliet0 wrote:

I ran CNVkit on bulk RNA samples using the import-rna flag. I generated the TCGA CNA/expression correlation files as directed and they look very similar to the example. I used HTSeq to generate my count matrices. I used only samples that passed QC and simply calculated the mean expression for each gene. I ran CNVkit on both raw and normalized counts to see if that made a difference, but unfortunately although the program runs perfectly fine, my output shows the same weight of 1.0 for all genes and the exact same predicted copy number (0.044394...) for all genes as well.

I'm thinking there might be lots of reasons for why my runs didn't pan out: maybe my data is too sparse after all (RNAseq on formalin-fixed tissue with baits), maybe I can try to use RSEM for quantification. I was just wondering whether anyone has specific advice for what I can try next.

import-rna cnvkit • 547 views
ADD COMMENTlink modified 22 months ago by Eric T.2.6k • written 22 months ago by a.v.vliet0
1
gravatar for Eric T.
22 months ago by
Eric T.2.6k
San Francisco, CA
Eric T.2.6k wrote:

It looks like there was a regression and import-rna is currently only working for RSEM files, not the 2-column format: https://github.com/etal/cnvkit/issues/425

Working on a fix.

ADD COMMENTlink written 22 months ago by Eric T.2.6k
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