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Should I remove scaffold when perform tophat and cufflinks ?

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!

rna-seq
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updated by Devon Ryan Devon Ryan • written by Pei Pei

1 answer

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.

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written by Devon Ryan Devon Ryan

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