How to compare RNA-seq counts matrices from different aligners ?
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Aurora ▴ 20
@aurora-15104
Last seen 6.0 years ago

I have used an aligner to produce raw counts from a publicRNA-seq data (GSE63310 , the counts are available online). I would like to compare my results with the "official ones" on the GEO website but I don't know how to compare accurately these two matrices to have an idea of their similarity.

Thank you for advices
rnaseq counts alignement • 1.1k views
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Are they in the same id name? Are they for the same sample? Then you can do a PCA for each matrix, and compare the results. Are the same samples near the same other samples?

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