demultiplex PacBio fastq file

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4.6 years ago

ieie ▴ 10

Hi everyone,

I have just got back my PacBio sequencing of fungal ITS2 amplicons. I received one fastq file and I need to demultiplex the data in order to perform the filtering the clustering. I have never performed demultiplexing so I would like to ask which pipeline could I use to demultiplex this dataset.

Thanks a lot for any help!

next-gen-sequencing sequence • 2.1k views

ADD COMMENT • link updated 17 months ago by Ram 44k • written 4.6 years ago by ieie ▴ 10

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Are barcodes in the header? Please add details. How many samples are in the file?

ADD REPLY • link 4.6 years ago by ATpoint 85k

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For PacBio data you can try their demultiplexing software LIMA.

Someone posted this a couple of days back: A: How to demultiplex PacBio from CCS.h5 or fastq You will need to see if this is correct.

ADD REPLY • link 4.6 years ago by GenoMax 147k

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You can also find a google group "SMRT_isoseq" to ask there specific questions.

ADD REPLY • link 4.6 years ago by tanya_fiskur ▴ 70

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