Hello,
I'm new to this area and I just wanted to confirm I'm not missing out on something important. I have RNA-seq strand specific, single end data generated using the duTP method. I want to align my raw reads to the reference genome and am using Bowtie2, version 2.0.2. I read the manual and these forums, but I'm still confused about which tag, if any, I have to supply to bowtie to let it know that I'm using strand specific data.
Reading the manual, makes me think --nofw/--norc, is not what I'm looking for, but I'm still unsure. I appreciate any help you can provide me with. And I'm sorry if the answer is really obvious.
Thanks.
I'm new to this area and I just wanted to confirm I'm not missing out on something important. I have RNA-seq strand specific, single end data generated using the duTP method. I want to align my raw reads to the reference genome and am using Bowtie2, version 2.0.2. I read the manual and these forums, but I'm still confused about which tag, if any, I have to supply to bowtie to let it know that I'm using strand specific data.
Reading the manual, makes me think --nofw/--norc, is not what I'm looking for, but I'm still unsure. I appreciate any help you can provide me with. And I'm sorry if the answer is really obvious.
Thanks.
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