How to use fastq subreads PacBio reference free for analysis

Question

[sam891]

Hello,

I downloaded subreads of RNA-seq in .fastq format and I need a pipeline that provides classification, clustering, polishing using this format because it is the only one that can be downloaded from the ncbi. Doing some research I noticed that the most used pipeline for RNA-seq subreads is Isoeq3 but unfortunately it only works if the subreads are in .bam format. I tried to convert fastq format to bam using picard.jar command

FastqToSam

but isoseq3 doesn't accept them because all the PacBio BAM requirements are missing. Does anyone know of an alternative pipeline? thanks a lot!

Sam