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LRGASP / lrgasp-submissions

Definition and validators for LRGASP submissions
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PB adapters #28

Closed Lutri22 closed 3 years ago

Lutri22 commented 3 years ago

Hi,

I would like to run the default Isoseq3 clustering pipeline on some of the PacBio data. I think to get the FLNC.bam file with the clusters I would need to provide the adapter sequences to lima. As far as am aware of it there is no way to do this from the provided fastq files? I would be interested if the fasta file containing the PB adapters (PB_adapters.fasta) available somewhere?

Many Thanks

diekhans commented 3 years ago

Hi, will look into this and get back to you.

diekhans commented 3 years ago

The vanilla PacBio adapters are as follows:

primer_5p AAGCAGTGGTATCAACGCAGAGTACGGGG primer_3p AAGCAGTGGTATCAACGCAGAGTAC

And the CapTrap PacBio adapters are these:

primer_5p TCGTCGGCAGCGTC primer_3p GTCTCGTGGGCTCGG

thanks for asking, we will add this to the documentation