I'm performing RNA-seq analysis. I have used Hisat2 for aligning reads to the genome and stringtie for quantification and extracted read count information directly from the files generated by StringTie using "prepDE.py" mentioned in Stringtie manual. With the counts data I have used edgeR for Differential analysis.
Before that I have seen MDS plot showing in the following way:
I see that three samples are not clustered and thought that they are not sequenced well. So I removed the three samples and again made an MDS plot.
Can anyone tell me what could be the reason for this type of clustering? Is that because of sequencing? or using count data directly from stringtie or anything else?