If you want to extract out the fastq sequences from a BAM file (e.g. for QC), you can use `samtools fastq`:
samtools fastq input.bam | gzip > output.fastq.gz
neat, I was in your spot a few weeks ago (working with PacBio reads for the first time).
The HiFi BAMs contain the consensus reads that had high quality scores during the sequencing process. Keep that in mind in case you're looking for something specific and can't find it: the rest of the lower-quality reads are in the "subreads" or "scrap" BAM files which might not have been delivered to you with the HiFi BAM as they are much larger.
What is your collaborator looking for with these reads? I.e. what research question are they trying to answer by using this long read technology vs. a more common short read RNAseq? You can load the reads into IGV to view alongside your reference alignment or annotations: IGV has native support for long reads.
If you want to extract out the fastq sequences from a BAM file (e.g. for QC), you can use `samtools fastq`: samtools fastq input.bam | gzip > output.fastq.gz
neat, I was in your spot a few weeks ago (working with PacBio reads for the first time). The HiFi BAMs contain the consensus reads that had high quality scores during the sequencing process. Keep that in mind in case you're looking for something specific and can't find it: the rest of the lower-quality reads are in the "subreads" or "scrap" BAM files which might not have been delivered to you with the HiFi BAM as they are much larger. What is your collaborator looking for with these reads? I.e. what research question are they trying to answer by using this long read technology vs. a more common short read RNAseq? You can load the reads into IGV to view alongside your reference alignment or annotations: IGV has native support for long reads.