Transcripts read count

Question

[philgev2]

Hi

Which is the most correct way to calculate Transcripts read count for differential transcript expression?

I have come across using RSEM software with bam file containing transcript coordinates.

Also using script prepDE.py provided by StringTie assembler that use bam file with genomic coordinates.

Can I opt any one of these option? Or should I use any other option?

Thanks Philge Philip

Answer 1

[andrew.j.skelton73]

Check out Kallisto -> Sleuth or Salmon -> Wasabi -> Sleuth for modern differential transcript expression solutions.