Tools for asserting matching pairs of samples from the same patient
In a RNA-Seq project, I have 10 samples, 2 each from 5 patients. I would like to make sure the patients or sample pairs were labeled properly and that there was no mix up.
I used the counts from HT-Seq to generate MDS and scatter plots to assess them. The plots suggest, there might be a mix up.
But I wanted to know if there are tools for such analysis, which take in FastQ or BAM files.
Any suggestions appreciated. Thanks!
2 answers
You could use DeepTools. It Accepts BAM files and plots a Principal component analysis of the coverage within bins of a size determined by the user.
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