Running IsoSeq pipeline

Question

[BDK_compbio]

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.

[Sparrow_kop]

Hi, "primers.fasta" is input file,which can be found in isoseq pipeline url link you wrote, because at usual the primer is universal primer, in fact you can validate this primer sequence by alignment with your reads. And "demux.bam" is the output file not input file. Hope this information could help you.