PacBio merge runs

Question

[firestar]

For one of my samples, I have two runs.

sample1
+-- run1/
|   +-- *.bax.h5
+-- run2/
    +-- *.bax.h5

My workflow involves using bax2bam to convert .bax.h5 to unaligned bam. Then using pbalign to convert unaligned bam to aligned bam.

How do I combine these two runs into one sample? And at what point in my workflow do i do that?

Answer 1

[firestar]

I managed to get it to work. Not sure if this is the best way.

I converted *.bax.h5 to BAM separately for each run.

bax2bam -o "sample1_run1" $(find . -name "*.bax.h5")
bax2bam -o "sample1_run2" $(find . -name "*.bax.h5")

This creates scraps and subreads BAM files. I merged the subreads BAMs.

samtools merge sample1.bam sample1_run1.subreads.bam sample1_run2.subreads.bam

Then created the .pbi index file using SMRT/5.0.1

pbindex sample1.bam