Trimmomatic adapters for TruSeq Nano DNA kit
0
0
Entering edit mode
9 months ago

Hello, 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.

data analysis NGS • 493 views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

yeah I ran fastqc before trimming. Thanks for clarifying. I will definitely check that.

ADD REPLY
0
Entering edit mode

I ran adapter trimming by using TruSeq3 but it gave very low alignment rate. Please help me in this

ADD REPLY
0
Entering edit mode

"It gave low alignment rate", does that mean alignment rate was better without trimming?

ADD REPLY
0
Entering edit mode

i didnt check that. Let me check once

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

hii, 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?

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

ok thank you so much

ADD REPLY

Login before adding your answer.

Traffic: 1851 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6