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Recent Replies
Comment: Differences between published differential gene expression results and own analy
by
vernonlim98
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Have included the links to the papers I mentioned in another comment for reference!
Comment: Differences between published differential gene expression results and own analy
by
vernonlim98
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0
These are the 2 papers I mentioned previously that used data other than raw counts for their analysis: https://onlinelibrary.wiley.com/doi/…
Answer: Collect COV file by BedCoverage
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Hello German , I am using clinCNV for WES and i faced the same error and this part of the error
[1] "ERROR: your file with normal coverage…
Comment: How to create a consensus of a contig with samtools or bbmap?
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marongiu.luigi
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sorry, I have mistaken samtools with spades... running `samtools view -h...` did the trick. Thank you.
Comment: Help with Ideathon
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V K
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Thank you for the response! Unfortunately this is completely independent and not part of a course. I was asking for some innovative ways to…
Answer: How to create a consensus of a contig with samtools or bbmap?
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You assembled a genome using samtools ???? that sounds very weird, if not impossible ...
The header (SQ lines) is missing from your file b…
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The XX and XY counts are present on any given variants page.
Comment: Help with Ideathon
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I don't see a single question here. Saying `I need your expert help in figuring out how I can make this analysis useful!` is too open-ended…
Comment: Differences between published differential gene expression results and own analy
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ATpoint
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Please link the paper, lets see their methods. With human data it can well be that they included something like surrogate variables to damp…
Comment: Differences between published differential gene expression results and own analy
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dsull
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There are many ways to do normalization and one of the correct ways is simply to plug raw counts into deseq2 (the math that deseq2 uses to …
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rfran010
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Is it the version number in your data?
e.g. ENST00000415118.1 vs ENST00000415118 could be causing the mismatch?
Comment: Differences between published differential gene expression results and own analy
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So is there any correct way for normalisation? I know limma recommends CPM via limma-voom and DESeq2 just takes in raw counts and does thei…
Comment: Gene expression equivalent of polygenic risk score ?
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Picasa
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Thanks a lot for your answer. I will check the paper.
Comment: Differences between published differential gene expression results and own analy
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dsull
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If those logFCs are different, then that's a normalization issue.
The logFC is straight forward arithmetic (it's simply dividing mean of […
Comment: Differences between published differential gene expression results and own analy
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vernonlim98
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Thanks both for your input. It got me to look at the published methodologies more closely, and you guys were right. One paper that I was re…
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