I'd like to inquire about the possibility of extending HipSTR with another stutter model in an attempt to cope with highly amplified STR loci originating from single cells. We've recently found (https://www.biorxiv.org/content/early/2018/05/08/065110) that by allowing a single degree of freedom (the number of simulated PCR cycles) we can accurately fit measured stutter patterns for most of our single-cell derived genomic loci. This was obtained using a contraction-biased stutter model, calibrated using NGS of a synthetic library .
We would very much like to use HipSTR and enjoy all its great features. Ideally, we would like to employ this model within HipSTR to adjust for the currently unavoidable amplification performed when processing single cells and we're wondering about your interest and availability to assist us in doing so.
We're also interested in attempting to better cope with unbalanced allele amplification that is the result of all current single-cell whole-genome-amplification protocols, using the haplotyping techniques developed by you if you would consider this advisable.
Thanks in advance
I'd like to inquire about the possibility of extending HipSTR with another stutter model in an attempt to cope with highly amplified STR loci originating from single cells. We've recently found (https://www.biorxiv.org/content/early/2018/05/08/065110) that by allowing a single degree of freedom (the number of simulated PCR cycles) we can accurately fit measured stutter patterns for most of our single-cell derived genomic loci. This was obtained using a contraction-biased stutter model, calibrated using NGS of a synthetic library . We would very much like to use HipSTR and enjoy all its great features. Ideally, we would like to employ this model within HipSTR to adjust for the currently unavoidable amplification performed when processing single cells and we're wondering about your interest and availability to assist us in doing so. We're also interested in attempting to better cope with unbalanced allele amplification that is the result of all current single-cell whole-genome-amplification protocols, using the haplotyping techniques developed by you if you would consider this advisable. Thanks in advance