Hi! I'm using Pinfish (https://github.com/nanoporetech/pipeline-pinfish-analysis) to identify transcripts. But I don't know whether the resulting transcripts in the "Merged_polished_transcripts_collapsed.gff" file are dependable?
As indicated in the igv snapshot, one read (red arrow) in the reversed direction has almost the same exons with other reads. Is there one possibility that this read is not correctly oriented in pychopper?
Another type of reads indicated by green arrow aslo have the reversed direction and are long reads. Could such reads be real full-length transcripts?
Here is the workflow for analysis:
After running "rule map_reads", I extracted the reads on specified chromosome and merge all the bam files from different samples, then run the following rules in snakefile (https://github.com/nanoporetech/pipeline-pinfish-analysis/blob/master/Snakefile). I modified the "minimum_cluster_size: 1" to preserve as many reads as possible.
Could anyone help interpret the above issues? I really appreciate your suggestions!
