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zd1 / telseq

A software for calculating telomere length
GNU General Public License v3.0
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Short telomere length output - NovaSeq samples #33

Open kacyng92 opened 2 years ago

kacyng92 commented 2 years ago

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.

kruthikaiyer0990 commented 1 year ago

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.

squigzzz commented 4 months ago

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.