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ajlabuc / meCLIP

Snakemake based analysis pipeline to identify m6As from eCLIP data
MIT License
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May I ask how to config if the adapter is not listed in the library ? #2

Closed LoneKnightz closed 1 year ago

LoneKnightz commented 1 year ago

Hi,

I am sorry to bother you again.

I have checked the document/Readme and it mentioned we should give the adapter sequence and name from eCLIP library.

But the data I have now is using TruSeq RNA adapter : AGATCGGAAGAGCACACGTCTGAACTCCAGTCA. ssDNA adapter: NNNNNNNNNNAGATCGGAAGAGCGTCGTGT

May I ask how should I modify the config files to make it work?

Or can I use cutadapt myself and then feed into the pipeline ?

Thanks

NanoCoreUSA commented 1 year ago

Hi @LoneKnightz

The pipeline automatically handles Illumina TruSeq adapters as is, I would just give it a go and as long you summary report shows the adapters were removed successfully you should be good to go.

LoneKnightz commented 1 year ago

Thanks!