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Recent Replies
Comment: inferCNV on Visium 10X: lower residual expression in tumoral spots (heatmap inte
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GenoMax
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Attaching a screenshot for ready reference. Full size PDF linked above.
Posted as an issue to InferCNV already: https://github.com/broadin…
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> local SSDs are cheap and very fast
And keep in mind that they will wear out, especially if you are writing TB's of data regularly.
Comment: Strandedness issues in STAR quantification
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Looks like you have already opened an issue on STAR repo: https://github.com/alexdobin/STAR/issues/2650
That was going to be the next sugg…
Comment: How to Remove Phasing Information from a VCF File?
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How can I use bcftools +setGT to get genotypes without phase e.g. "|" or "/"?
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That is exactly what Snakemake is for.
You could create a `sample` variable at the top of a `config.yaml` file and loop over these samples…
Answer: Exome data analysis computing resources requirement query
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What others have said, but also
- whats your approx budget?
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Comment: Strandedness issues in STAR quantification
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I tried STAR counting with an index created without GTF. The results are identical to those based on index created with GTF. Every single c…
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You can get some data from GDC portal: https://portal.gdc.cancer.gov/analysis_page?app= and https://portal.gdc.cancer.gov/analysis_page?app…
Comment: TCGA MSI status
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Can I get TCGA somatic mutation vcf files or maf files
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What kind of technology is this data from? If it is Parse tech data then you may need to use their pipeline that you can get from here: htt…
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> duplicated genes
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Yes, the y-axis is reasonable. ALthough the test for differences should come from DESeq, rather than from a wilcox in this case. With four …
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saruman
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Done. Thank you.
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Far as I know TCGA did not do transcript level expression as a standard analysis (see the list here --> https://docs.gdc.cancer.gov/Data/Bi…
Comment: [VG sim, surject, giraffe] How to remove a sample from GFA/GBZ graph
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GenoMax
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https://www.biostars.org/u/45375/ : Please accept this answer (green check mark) to provide closure for this thread.
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