Should I remove scaffold when perform tophat and cufflinks ?

Question

[Pei]

Hi all:

I am going to perform RNA-seq analysis in one plant. but the genome provided was with many scaffolds, I suspect that redundancy could NOT be ignored or underestimated.

So, do you think I can ignore all scaffolds and only use known chromosomes when perform tophat and cufflinks ?

Thanks in advance! Best wishes!

Answer 1

[Devon Ryan]

As a general rule, it's best to include scaffolds and other unplaced genomic elements in the alignment. As long as they actually exist somewhere in the genome, you'll get more false-positive alignments if they're removed.