Read metadata from a pacbio bam file

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6.9 years ago

biomagician ▴ 410

Hi,

I have got a BAM file from PacBio data and would like to read some of the metadata of reads in R, e.g. ip, pw, rq. See here for pacbio BAM format: http://pacbiofileformats.readthedocs.io/en/3.0/BAM.html

I have read the BAM into R with Rsamtools::scanBam('file.bam') and I have got a BAM file in R now but I don't know how to extract the ip, pw, rq info.

I have no problem extract sequencing info, mapq, flag and usual BAM tag. It's the metadata that I have a problem with, the additional columns in the BAM file.

I hope someone can help.

Thanks.

C.

bam pacbio rsamtools sam R • 3.2k views

ADD COMMENT • link 6.9 years ago by biomagician ▴ 410

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You may be better off using SMRTanalysis v.3.x for this purpose.

ADD REPLY • link 6.9 years ago by GenoMax 141k

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I've started using SMRTLink in a browser, do you know if it's the same thing? http://www.pacb.com/wp-content/uploads/SMRT-Link-User-Guide-v4.0.0.pdf

ADD REPLY • link 6.9 years ago by biomagician ▴ 410

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Yes. If you want to work with PacBio specific data like what you describe above this would be the best option. It is called SMRTlink now instead of SMRTanalysis (old name).

ADD REPLY • link 6.9 years ago by GenoMax 141k

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