John Harting

as this is largely been deprecated and there are no specific blocks to using anything other than PacBio data, I don't think this would be an issue for anyone. use...

The python parts of the Pacbio software stack are just now being updated to version 3.7, including pbcore. The repeat analysis scripts are still v2.7 until I can get them...

Hi Wen, The -E 0 parameter causes the gap-extension penalty to be a constant, rather than linearly increasing cost. Long expansions relative to the reference may not map *through* the...

Hi, Sorry for the slow response! My first suspicion when you say soft-clipped reads is that you might have some palindromic reads in your data. This can happen when you...

The last line of the traceback is looking for an index. Does your input bam file have a .pbi index associated with it?

Apologies for the delay -- does your reference also have an .fai index associuated with it? Can you try to run pbvalidate on your aligned bam? `pbvalidate --aligned --index --reference...

It looks like the bam you are using does not match PacBio specifications. What mapping program did you use to generate the alignments? You should be able to use the...

Looks like you might not have the sequencing chemistry set properly in your bam header. If you call `samtools view -H [your bam]` on your input bam, what are the...