Number of Wheat transcript varies

Question

[K S]

Hi,

The number of transcript for wheat genome varies between IWGSC and Phytozome databases?

IWGSC
High confidence             Low confidence
104,696                          100,947

Phytozome (v13)
Triciticum v2.2 has 293, 053

Why the difference is three fold? Which one to be considered for the sRNA read mapping?

Thank you

Answer 1

[JC]

Seems like both are independent transcripts reconstruction, if the data comes from RNA-seq and doing de novo transcript assembly is common to have >100k transcripts with Trinity, Oases, SPAdes-rnaseq or similar tools. Why are you using transcripts for sRNA reads mapping? In general, those data sets don't contain sRNA genes (too short to be reconstructed). I would use the genome.

[JC]

I see the comments in another post from you, if you are fine using the microRNAs or similar sRNA families to do the mapping that is fine.