I am analyzing Pacbio data for the first time and I have the following files
1) ..fastq.gz 2) ...sts.xml 3) ...subreadset.xml 4) ...subreads.bam 5) ...subreads.bam.pb
I am following the IsoSeq pipeline given here. I finished the "Generate CCS" step by executing "ccs" command. But for "Classify full-length reads" (using "lima"), I think "primers.fasta" and "demux.bam" files are needed.
So I am wondering how can I get these two files? Do I need to ask the sequencing company to provide me with these files? Is this step mandatory before clustering step?
Any help would be appreciated.