Short telomere length output - NovaSeq samples
Opened this issue · 2 comments
Hi,
Recently I used TelSeq to estimate telomere length from WGS sequencing data (NovaSeq), with k = 7 and r = 151. The returned length falls in the range of 0.4 - 0.5kb. However for a different batch of samples (HiSeq) with the same parameters, the returned length is from 5kb to 15kb.
When I checked the output files, I could see the amount of TEL0 - TEL1 - TEL2 reads were much higher in NovaSeq samples compared to HiSeq samples (also the mount of TEL10+ was lower in NovaSeq samples). I troubleshooted by reducing k to 4, which helped increase the length to 1.4kb, but this is still not the normal range of telomere length.
May I know if you have experience with running NovaSeq samples before, and I kindly seek for recommendation to fix this short telomere length issue. Thank you very much! Your help is greatly appreciated.
Hi!
Were you able to resolve this issue? If yes, what threshold for k did you end up using?
I'm experiencing something similar with my WGS bams sequenced using NovaSeq with a read length of 150bp.
I am having similiar issues with WES data generated with NovaSeq with a read length of 150 bp I am getting length estimates down to the 3rd or 4th decimal place which make little sense.