I've been experimenting with HISAT-3N because I'm analyzing some SLAM-seq and TimeLapse data (both PE) and unfortunatly Slamdunk is not compatible enough. Nevertheless I was wondering if there's anyway an option (or additional function) might be added to generate some type of count matrix for reads containing conversions instead of just the number of conversions per position.
This will be very useful for downstream analyses and (if I'm not wrong) at the moment there are not many options to easily generate this type of outputs coming from HISAT-3N aligned data, limiting its use.
Also, any recommendations to deal with this in the meantime would be very helpful :)
Hello,
I've been experimenting with HISAT-3N because I'm analyzing some SLAM-seq and TimeLapse data (both PE) and unfortunatly Slamdunk is not compatible enough. Nevertheless I was wondering if there's anyway an option (or additional function) might be added to generate some type of count matrix for reads containing conversions instead of just the number of conversions per position. This will be very useful for downstream analyses and (if I'm not wrong) at the moment there are not many options to easily generate this type of outputs coming from HISAT-3N aligned data, limiting its use.
Also, any recommendations to deal with this in the meantime would be very helpful :)
Thanks!