Read metadata from a pacbio bam file

Question

[biomagician]

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.

[GenoMax]

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

[biomagician]

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

[GenoMax]

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).