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sorry, I have mistaken samtools with spades... running `samtools view -h...` did the trick. Thank you.
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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…
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The XX and XY counts are present on any given variants page.
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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…
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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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Is it the version number in your data?
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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…
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Thanks a lot for your answer. I will check the paper.
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If those logFCs are different, then that's a normalization issue.
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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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Yes it does not match at all, and those genes that are common in both analysis results have very different logFC and p values
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I am not sure what you mean by this, but I believe that is what I did. With Trinity, I matched all the paired reads together, so they shoul…
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I don't think something exists out of the box. With variants, we have a 'weight' for each variant on disease risk (obtained through large s…
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