I am working on bacterial data whose library preparation kit used is TruSeq Nano DNA. I am confused which Trimmomatic adapters shall I use for TruSeq Nano DNA kit - TruSeq2 or TruSeq3 or Nextera? Please help me. Thanks in advance.
It should be the TruSeq3. The Nano kit has the TruSeq adapters, but workflow is optimized for low input amounts, but this has nothing to do with the adapter sequence itself. Be sure to run fastqc before and after trimming to confirm proper adapter trimming.
yeah I ran fastqc before trimming. Thanks for clarifying. I will definitely check that.
I ran adapter trimming by using TruSeq3 but it gave very low alignment rate. Please help me in this
"It gave low alignment rate", does that mean alignment rate was better without trimming?
i didnt check that. Let me check once
It is still not working. I am looking for adapter sequences but I am not getting it. From fastqc I got to know that the adapters are from SOLID small RNA adapter. can anyone explain me how to deal with this kind of adapter? Library kit usd is TruSeq nanoDNA kit.
I got adapter sequences for truseq nano DNA from sequencing providers only but after using these adapters, I am getting 0.05% alignment rate. I used hisat2 for alignment and trimmomatic for adapter trimming. Can you please tell me what's wrong with my process?
Look, I cannot see your data therefore I do not know. It is actually simple. If you have adapter contamination and then trim it, and confirm by fastqc that they're gone, and you still get poor alignment then it is not due to adapters but either poor libraries or a flawed alignment pipeline. With the given information there is not much more to tell.
ok thank you so much
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