Hello all,
I have a question regarding Illumina adapters. I'm a grad student coming into a previously uncompleted de novo assembly project. The sequencing was done commercially over a year ago so I have limited access to the specifics of what was ordered. What I do know is that I have 24 million paired end reads of 100bp length each. From what I can tell just purusing the sequencing company's website is that they use a HiSeq2000, though I can't be 100% confident this is the machine used to generate my reads.
My question concerns the adapters and whether or not trimming is neccessary. My understanding is that sequencing of the DNA fragment begins after the adapter and so the only way to have actual adapter sequence in my reads is if the read length was greater than the fragment size and read into the adapter on the opposite end. Is this a correct assumption? Is this assumption valid for all Illumina machines (MiSeq, GA, etc).
Basically I'm just trying to figure out if I need to do any adapter trimming before attempting assembly. The FastQC report provided with my reads does not show any overrepresented sequence, though I don't know if the company used a TruSeq kit which I beleive are the adapters FastQC looks for. Any help / insight would be greatly appreciated.
I have a question regarding Illumina adapters. I'm a grad student coming into a previously uncompleted de novo assembly project. The sequencing was done commercially over a year ago so I have limited access to the specifics of what was ordered. What I do know is that I have 24 million paired end reads of 100bp length each. From what I can tell just purusing the sequencing company's website is that they use a HiSeq2000, though I can't be 100% confident this is the machine used to generate my reads.
My question concerns the adapters and whether or not trimming is neccessary. My understanding is that sequencing of the DNA fragment begins after the adapter and so the only way to have actual adapter sequence in my reads is if the read length was greater than the fragment size and read into the adapter on the opposite end. Is this a correct assumption? Is this assumption valid for all Illumina machines (MiSeq, GA, etc).
Basically I'm just trying to figure out if I need to do any adapter trimming before attempting assembly. The FastQC report provided with my reads does not show any overrepresented sequence, though I don't know if the company used a TruSeq kit which I beleive are the adapters FastQC looks for. Any help / insight would be greatly appreciated.
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