Many Dangling end pairs

[HiC-Pro]

Hi Nicolas

I am trying to process the Cortex HiC dataset which uses HindIII restriction enzyme using the HiC-Pro, but I am getting many Dangling end pairs (about %50). Do you have suggestions for the parameters MIN/MAX_INSERT_SIZE, MIN/MAX_FRAG_SIZE, MIN_CIS_DIST that could help decrease the number of Dangling end pairs?

Thanks
Sajid

[nservant]

Hi Sajid,

All these parameters do not change the number of DE. The pairs which are discarded because of these values are classified as "dumped pairs".
Dangling reads correspond to fragment which are not ligated. There is no way to improve it ... unless redoing the library prep !
Best

[wenhong jiang]

I also got the problem.But what the dangling reads are?As you said m it came from fragment failed to ligated, then it would be a single read which have not the other read to become a pair.So the fragment would be sington other than dangling reads.Am I wrong?Can you draw a picture to explain them?(if FF-pairs RR-pairs FR --RF pairs explained ,many thanks)

THANKS !!!

在 2017年6月21日星期三 UTC+8上午1:09:37，nservant写道：

[nservant]

Hi,

Unligated fragments do not mean singleton.
Singleton are usually due to mapping issue. Unligated fragment are still sequenced as normal PE reads.
We can detect them because both reads are aligned on the same restriction fragment.
You can have a look to this figure which summarize the main idea
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4347522/figure/F2/