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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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Perform hichip and found that high trimmed map rate to 50% #545

Open chase2biye opened 1 year ago

chase2biye commented 1 year ago

Hello I performed hichip and ran HiC-Pro, the results show that my sample have higher trimmed map rate to around 50%. According to the manual :"abnormal level of chimeric reads can reflect a ligation issue during the library preparation", but I cannot understand the machanism of this problem and how to imporve my experiment. best wishes

garbikk commented 1 year ago

Hi, I met the same problem. Did you ignore it and continue to analyze or redo the experiment? Thank you very much.

chase2biye commented 1 year ago

Hi, I met the same problem. Did you ignore it and continue to analyze or redo the experiment? Thank you very much.

I continue to analyse and did not find any problem so far

garbikk commented 1 year ago

Hi, I met the same problem. Did you ignore it and continue to analyze or redo the experiment? Thank you very much.

I continue to analyse and did not find any problem so far

I see. Thank you for your reply.