in ORF finding, is minus strand correct?

Question

[m.pezhmanmehr]

Hi I use ORF finder for finding CDS of my transcripts. always I choose longest and + strand. but sometimes longest strand is - (minus). Is minus strand correct too? thank you

Answer 1

[h.mon]

Was the library prep strand-specific? How did you assembly your transcripts? Meaning: if your library prep was strand-specific, and you used a transcriptome assembler capable of using reads in a strand-specific manner, then I would think no, the longest orf on minus strand are most likely artifacts.

Using BLAST may help decide if the minus strand longest orfs are artifacts or real CDS.