Question: Read metadata from a pacbio bam file
0
gravatar for cristian
2.9 years ago by
cristian240
cristian240 wrote:

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.

sam rsamtools pacbio bam R • 1.5k views
ADD COMMENTlink written 2.9 years ago by cristian240

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

ADD REPLYlink written 2.9 years ago by genomax80k

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 REPLYlink modified 2.8 years ago • written 2.8 years ago by cristian240

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 REPLYlink modified 2.8 years ago • written 2.8 years ago by genomax80k
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