Orientation of RNA-seq reads

[jack84]

Hi,

I have a question about the orientation of a RNA-seq read. For example, in a fasta file I have an entry:

@SRR034096.2 HWI-EAS6_2_FC200R3:4:1:397:22 length=33
GGGGATATGGCGAAATCGGTNTCGTATGCCGNC
+SRR034096.2 HWI-EAS6_2_FC200R3:4:1:397:22 length=33
IIIIIIIIIIIIIIIIHII,!IIIIFDI=DI!I

So for this read, is the orientation always from 5' to 3'? That is, The first 'G' is the 5' end and the last 'C' is the 3' end.

Thanks and best regards,

Jack

[mastal]

Orientation of RNA-seq reads

Yes, but unless the read is from a strand-specific RNA-seq protocol,
the read/transcript could be from either DNA strand.

maria