Cutadapt or Trim Galore for SMART-seq?

Question

[Youyy]

Hi, I am recently processing a SMART-seq paired end illumina data on Galaxy. Which tool is the best to trim the raw data? Cutadapt or Trim Galore?

Cutadapt has the parameter setting that asking you to specify the 3' and 5' adapters for both Read1 and Read2. I will add the SMART-seq 3' adapter and illumina universal adapter to the 3', and add SMART-seq 5' adapter to 5', for both Read 1 and Read2. As the picture belows, is my setting correctly? Trim Galore can auto-detect adapters (Does the auto-detect trim the SMART-SET adapters?), someone just told me that it has the similar setting. As the picture shows, but it seems that it doesn't specify 3' or 5'. If I specify the smart-seq adapters here, can it sill detect illumina universal adapters?

Thanks

[ATpoint]

Look, this behaviour of deleting posts that received comments already is not acceptable. A user invested time, just deleting it is disrespectful. You can ask for clarification in the existing thread, I am going to delete the new question you just opened. Basically you could have asked this question here already in the previous one which was about the same topic.

[Youyy]

Sorry, because I edited my question a lot, so I started a new one.

[ATpoint]

No problem, but as said, please do not do that. It wipes out the efforts of everyone who contributed and will annoy people so they might stop even reading your posts.

[gb]

Trim Galore has the same option (https://usegalaxy.org/) The parameter named "Adapter sequence to be trimmed" can be changed from Automatic detection to User defined.

[Youyy]

Thank you. I found the option. But, if I specify Adapter sequence to be trimmed off read1 and read2, does the Trim Galore still to be able to detect illumina universal adapters? thanks.

[gb]

I don't think so but it is easy to run a tool twice in galaxy. So maybe that is the best option. I moved my original answer to the comments because I see the question is changed now.

[Youyy]

Thank you.