Counting step includes all reads feed in in the BAM

[callumparr]

1. Is there any filtering steps of reads going from the BAM alignment file to final transcriptome assembly. I.e. are some reads discards because they fail some QC filter like fraction coverage or read identity?

2. related to no.1. Is the counting at the end based on all reads from the original BAM files or only counting reads that were used to assemble the transcripts?

[andredsim]

Hi there,

Sorry for the delayed response.

1. All reads in the bam file are used to identify novel transcripts as we do not filter them out based on the statistics you mentioned. However reads may end up not contributing to the final transcriptome assembly for other reasons such as the transcript not having enough read support. the full explanation of how this filtering works is best left to the manuscript (the updated preprint should be coming soon).
2. All reads are used for quantification, even if they do not contribute to the final transcriptome assembly. An example of this occuring is partial reads which may only overlap some of the exons of a transcript.