PacBio RSII reads

Question

[gina]

I am working with older PacBio data from 50 SMRT cells sequenced with the RSII technology. I used PacBioSuite-6.0.0.47841-1 bax2bam to create bam files. The size of the resulting subreads and scraps files is 219 Gbytes of subreads (6.4 million reads) to 298 Gbytes scraps. Is that an acceptable/normal/expected ratio of subreads to scraps? What is the best way to assess the quality?

Answer 1

[lieven.sterck]

sounds OK to me. In my experience I usually got much more scraps than subreads, so if your numbers are correct consider yourself lucky.

it's kinda hard to asses quality on raw reads (== unmapped) , so you either try to map them on a reference to examine the quality or you just take them as they are.