PacBio merge runs
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?
1 answer
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
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