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Old 06-15-2014, 10:45 PM   #2
Location: Germany

Join Date: Mar 2011
Posts: 68


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.
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