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Old 06-15-2014, 10:55 PM   #3
Location: La Jolla

Join Date: Nov 2013
Posts: 17

Originally Posted by Robby View Post

with help of strand specific RNA-Seq you can analyse, which strand was transcribed. This depends on the information to which strand a read maps and if it is the first or second read of the pair. You can't distinguish between the strands with help of the fastq files. For Illumina sequening all forward reads will be in one file and all reverse reads in the other file.
Hi Robby. Thanks for your reply. So for example if I have paired end RNA seq. All reads in the first fastq file are forward reads, all reads in second fastq file are reverse reads. Then if I map reads to reference genome, all reads in the first file should map to the forward strand of reference, and all reads in the second file should map to the complement strand of reference, right?
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