I have been successfully using tool ipdSummary.py, which reported me tMean value for each position in the reference (=average incorporation time of the nucleotides on that specific position). This worked well so far.
However, now I need to get individual values that are used to calculate tMean.
For example, if there are 5 reads aligning to the certain position in the reference, then tMean has been calculated from 5 values. I want to get these 5 values.
Alternatively, how could I get IPDs with respect to my reads instead of my reference? That way, for each read, I would have vector of IPD values in the length of the read (this would need to account for frequent errors in the reads, especially insertions which I need to skip for this purpose because they don't align to the reference).
Tagging rhall who may be able to answer this.
Thank you. Do you have any other ideas where to look for help, please?