PacBio Fastq file

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7.1 years ago

José ▴ 10

Hello, Last week I've received the genome PacBio data from a grass. I have a few questions about the data. -The provider give me a file with only the Filtersubreads (Filter=single pass and remove adapters) in Fastq format. There is ok or the must give me more data? maybe .h5? -The fastq subreads have an exclamation mark (The poorest value) as quality score, i don't know why, it's ok? I run FastQC and all the data have the same value.

The provider says me that the data have %85 of accuracy. It is ok for PacBio data, but i can't measure it.

Thank's

José

genome sequencing next-gen • 5.3k views

ADD COMMENT • link 7.1 years ago by José ▴ 10

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What is it that you want to do with this data?

Grab a copy of the original (*.h5) data files. Those would be needed for some software/analyses. Also ask your provider to run RS_ReadsOfInsert workflow which will give you consensus sequence for those subreads.

ADD REPLY • link 7.1 years ago by GenoMax 141k

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As genomax said, you'll want to dig deeper to make sure you are working with consensus sequence from the subreads. There are plenty of resources for working from .bax.h5 files:

Pacbio: extract fastq from h5 file based on quality filtering

Brent Wilson, PhD | Project Scientist | Cofactor Genomics 4044 Clayton Ave. | St. Louis, MO 63110 | tel. 314.531.4647 Catch the latest from Cofactor on our blog.

ADD REPLY • link 7.1 years ago by brent_wilson ▴ 140

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