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Posts by plat
... I am not used to bbduk but I think if you cut the adaptors the length should not be the same. Some reads would be cut by for instance, 5 nucleotides, others 10, and others not cut at all. This is why the length distribution should not be the same. ...
... I would recommend you to input your raw counts into DESeq2, run the pipeline, convert normalized reads to rlog (regularized log transformed reads) and then just run the plotPCA function from DESeq2. It is very easy if you are familiarized with the program. # Creating deseq2 object dds &l ...
... I think conservation depends on the species (or strains) you are looking for (e.g conserved from yeast to human). For that you have to set sequences from different species/strains that make sense (in the yeast example, for instance, yeast, fly, mouse and human) and construct a MSA with these sequenc ...
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