difference of tandem repeats counts between PCR-based data and PCR-free data

[doedoe0607]

Hi! Thank you for developing this tool.

I try to use EHDn to detect tandem repeats in our samples. These samples were sequenced from PCR-based libraries (2 × 100 bp paired-end reads) , which were different from the data (2 × 150 bp paired-end reads from PCR-free samples) in the published article (Trost et al, 2020). And they detected more apparent tandem repeats in samples sequenced from PCR-based libraries.

This phenomenon is also observed in our data, the 150bp PE (PCR-free) data of the same sample detected less tandem repeats than the 100bp PE (PCR-based) reads (2909 vs 811). We are very confused about this issue.

I noticed that you mentioned in your introduction that short (100-200bp) sequencing data is suitable, but I'm still not sure if we can try to analyse these data (100PE, PCR-based). What do you think may be the reason for this difference? We would be very grateful if you could give us some advice.
Thanks in advance.