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GaoLabXDU / HiSV

HiSV: a computational pipeline for structural variation detection from Hi-C data
MIT License
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On the problem of standard sets #5

Open TomWang666 opened 1 year ago

TomWang666 commented 1 year ago

hi,

When I read your article, I saw that HISV achieved high recall and precision in detecting inter translations of K562 and T47D. I also noticed that your standard set comes from the article "Integrated detection and analysis of structural variation in cancer genes" . However, I am confused whether it comes from the least two of (Supplementary Table 3, Table 4, Table 5) or from Supplementary Table 6. I don't know if you can help me solve my doubts.

Thanks for your help, Wang

GaoLabXDU commented 1 year ago

Hi Wang, High-confidence SVs for K562 and T47D cell lines were obtained by selecting intra-chromosomal SVs larger than 1Mb and inter-chromosomal translocations from Supplementary Table 6 in this article. Hope my answer can help you. Li

TomWang666 commented 1 year ago

Hi Li,

Thanks for your reply! But I still have some confusion. Does "SVs compared to 1MB" mean that the difference between the positions of two breakpoints is greater than 1MB? If so, in Supplementary Table 6, the T47D cell line has 9 eligible SVs, but in the supplementary material of HISV, a total of 16 intra SVs were detected. Then, I ran HISV to detect T47D at a resolution of 50kb, only 8 intra SVs were detected. So I'm confused, is the result of HISV detection integrated at multiple resolutions?

Thanks, Wang

GaoLabXDU commented 1 year ago

Hi Wang,

  1. When filtering eligible SVs in Supplementary Table 6 , did you ignore intra-chr-unclassified-BND type？If it is convenient, you can provide your email address and I can send the True positive datasets to you.
  2. HiSV does not integrate the results of multiple resolutions. When you run T47D sample, what other parameters do you set?You can try to adjust the cut-off parameters to obtain more SVs.

Thanks, Li

TomWang666 commented 1 year ago

Hi Li,

Thanks for your reply! My email address is 1127312621@qq.com. This is really important to me, thank you for your generosity!

Thanks, Wang

TomWang666 commented 6 months ago

Hi Li, Sorry to trouble you, I found that there is an error in the chromosome information of MCF7 in the standard set file you sent me. Could you please send me another standard set when you have time? My email is 1127312621@qq.com.Thank you very much!

Thanks, Wang