Dear ichorCNA team,
First of all thanks for the well-supported and useful tool.
I am looking to run ichorCNA on simulated 0.1X and 1X WGS ctDNA samples, obtained by aligned reads subsampling. Given that my samples have been sequenced using a paired-end protocol, when I compute the number of reads necessary to obtain the desired coverage should I consider the total number of paired-end reads or the total number of fragments (two fragments/ends for each read)?
I have looked through supplementary materials and I have found the description of 'Supplementary Data 1': I see that you use 'PF_READS_ALIGNED' in order to compute coverage, but even though I have looked into the corresponding supplementary table, I don't understand whether this parameter refers to the total number of paired-end reads, or to the total number of sequenced fragments/ends.
Dear ichorCNA team, First of all thanks for the well-supported and useful tool. I am looking to run ichorCNA on simulated 0.1X and 1X WGS ctDNA samples, obtained by aligned reads subsampling. Given that my samples have been sequenced using a paired-end protocol, when I compute the number of reads necessary to obtain the desired coverage should I consider the total number of paired-end reads or the total number of fragments (two fragments/ends for each read)? I have looked through supplementary materials and I have found the description of 'Supplementary Data 1': I see that you use 'PF_READS_ALIGNED' in order to compute coverage, but even though I have looked into the corresponding supplementary table, I don't understand whether this parameter refers to the total number of paired-end reads, or to the total number of sequenced fragments/ends.
Thank you in advance for your time