Customized adapter trimming for WGBS Galaxy(.eu) Workflow

usegalaxy.eu support
#1

Hello everyone.
I am doing a WGBS (Whole Genome Bisulfite Sequencing Analysis) and would like to adjust an existing workflow such that I am able to manually input strings for customized trimming in the adapter-detection step. The trimming tool used is Trim-Galore. The adapter sequences that I need to remove are shown below:
PrefixPE/1
TACACTCTTTCCCTACACGACGCTCTTCCGATCT
PrefixPE/2
GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
PE1
TACACTCTTTCCCTACACGACGCTCTTCCGATCT
PE1_rc
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
PE2
GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
PE2_rc
AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC

Would this task be possible? How would I facilitate this change on an existing worfklow? Thanks in advance.

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#2

Welcome, @npabusta , look for " User defined adapter trimming" in the tool page.

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#3

Thanks for your answer David!

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#4

You’re welcome :+1:

#5

Capture

@David Hi David, if I could ask one more follow up question… Out of the 6 adapter sequences I have shown in my initial post, which ones would I need to copy onto these sections: “Adapter sequence to be trimmed off” and “Adapter sequence to be trimmed off read 2”? Additionally, I am not too sure what the difference is between terms such as PrefixPE/1 and PE1rc so if you could clarify what that is as well, that might answer my question. I have attached a screenshot of the workflow tool editor under Trim-Galore. I hope it can be seen okay. Thanks again.

#6

@npabusta , You’ll find all the parameters and instructions in the TrimGalore documentation.

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#7

Hi @npabusta,
since you have multiple adaptor sequences, I suggest you use cutadapt instead of Trim Galore, becuase it allows setting multiple adapter sequences. In addition, cutadapt is the tool on which Trim Galore relies, and has been updated recently.

Regards.

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