Create CSS with different adapters

[JMir]

Hi!

I've searched for a similar thread and wasn't able to find a solution so I hope that this question is not repeated.

I am sequencing some SMRT library that contains the PacBio SMRT sequencing adapter in one end of the reads and a different adapter in the other.
I would like to create a CCS from these and I haven't been able to find any software that helps me doing that.

I have been looking to SMRT Link, which works only with SMRT adapters. Is there a way to introduce a custom adapter sequence?
I have also tried BBMap but I could only trim the adapters that are on the ends of the reads, not on the middle of them in order to create the CCS.
I was thinking on generating a custom script to do that but I find some difficulties like the mutation of sequencing, etc.

Can someone help me to find a useful software for my problem?

Thank you very much!!

[Zhangxj]

Hi, JMir

Has your problem been solved? I'm searching the same thing.

We are trying to use some different adapter, maybe asymmetric with other side. So we have to clip new subreads from polymerase read.

I find the software recalladapter, not sure it works.
https://github.com/PacificBiosciences/recalladapters

Thank you, and good luck.

[JMir]

Hi Zhangxj,

I have not been able to solve this problem.
After all this time, we changed the whole methodology also due to some other experimental problems so we are no longer looking for this kind of software.

Despite this, in the new methodology, I use HMMs to detect some small sequences, which perform quite good even though sequencing error, so maybe this can help you with the creation of your own method to detect the different adapters.

I hope you can find a solution.
Thank you for your reply,


Júlia

[Litamahadee]

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