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4

Going VCF to mpileup is not really something one does or can do. The mpileup should be generated from a BAM or SAM file or something else that has raw, unfiltered read alignments in it. The VCF just has data on variant sites, and usually just variant sites that passed a certain likelihood threshold at that. With the VCF, the best you can do is generate a ...


3

When I try this as a regular user on our Ubuntu 16 LTS system, I end up with ~/.local/bin/CIRIquant from the pip install, so maybe just add that directory to your path: $ export PATH="$HOME/.local/bin:$PATH" $ CIRIquant -h usage: CIRIquant [-h] [--config FILE] [-1 MATE1] [-2 MATE2] [-o DIR] [-p PREFIX] [-t INT] [-a INT] [-l INT] [-...


1

condition_IT_vs_control gives the effect of condition, conditionIT.time is the interaction of condition and time. If you wanted to test the effect of time, use name="time".


1

In this situation, you can apply the strategy in section 2.12 in the edgeR manual which basically "makes up" a dispersion estimate and then run the normal DE strategy. This is obviously neither reliable, nor publishable but at least it gives you a list of genes you can use for validation. Treat results with care, focus on genes with decent counts (...


1

According to DESeq2, you cannot analyze your data without having replicates. In short, you have an experiment where you compare A to B because, in your theory, A is more expressed than B. However, you do the experiment only once. Without repeating the same experiment again under the same circumstances, there's no way to confirm you will have the same results ...


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