Tools for asserting matching pairs of samples from the same patient

Question

[Jordan]

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!

Answer 1

[tiago211287]

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.

[Jordan]

That's the kind of tool I was looking for. Thanks!

Answer 2

[dariober]

Rather than passing by BAM files, it may be faster and better to quantify transcripts with an alignment-free program like Kalisto and do a PCA or MDS plot on the transcript expressions.