I used the pipeline-pinfish-analysis (https://github.com/nanoporetech/pipeline-pinfish-analysis) to analyze the ONT cDNA sequencing data to identify gene transcripts and isoforms. I donn't know whether the workflow is run correctly in my hand. For instance, I get no transcripts in the 'polished_transcripts_collapsed.gff' file shown in the igv snapshot. In the 'SRR22730723_reads_aln_sorted.bam' file, there are reads converage, but why the converage disappeared in the 'polished_reads_aln_sorted.bam' file.
The data I used is downloaded from SRA. I directly use the data for pychopper processing and then downstream pinfish analysis. Should the data be processed before these steps?
Hopefully I can get your suggestions!
bam file showing the alignment:
the dataset downloaded is filtered FASTQ:
