Hi
We have one batch which was done with single ended illumina reads and the rest paired. I ran salmon paired end mode for the other batches then changed to single ended mode for the singled ended reads. I then imported all the data together using tximport. I then did VST using DESEQ2 and did a PCA and the single ended reads are in their own cluster away from the rest of the samples. So it seems there is a batch effect, is this to be expected?
Kind Regards,
Chris
OK thanks again Gordon.