Hi! I have 2 samples swapped in a PCA of mRNA seq data of 4 genotypes and 3 replicates each: Col0.1 and tbl29.1.
I tried to use VCF files to look for variants, but I do not see any variation. The mutation is an insertion of 639 bp.
I tried IGV with bam files (and also VCF) but I do not see huge differences in alignments. With DESeq2 I saw the mutated gene (tbl29) is not expressed in all the replicates (and it´s ok, it can happen, but then I don´t know how to use these mRNA data for determining the swapped samples)
I am getting a bit crazy to demonstrate, on a genotype analysis, that I swapped the 2 samples.
Perhaps someone already experienced that and can give me suggestions? I am sure I am doing a very stupid mistake. Thank you very much!