search

nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
Other
382 stars 183 forks source link

chromosome interaction deletion #475

Open dqq20 opened 3 years ago

dqq20 commented 3 years ago

Hello！ I used hicpro-3.0.0 to deal with HiC,but there are some chromosome interaction deletion in chr17 70.3-70.5kb and 71.5-72.0kb, I don't know why? Here are my config.hi config-hicpro.txt cpro

dqq20 commented 3 years ago

patient_new-chr17 ofBins(3400-3600) 20K

nservant commented 3 years ago

Hi, I guess this is a repeated region with a very low mappability. So basically, almost no reads are aligned on this region. That's expected ;) N

dqq20 commented 3 years ago

Hi, I guess this is a repeated region with a very low mappability. So basically, almost no reads are aligned on this region. That's expected ;) N

But I want to show this region,how should I do?

nservant commented 3 years ago

You can still remove the filtering of multiple hits (RM_MULTI=0) in the config, but be careful with the interpretation, as the reads aligned on this region can come from another homologuous region, elsewhere on the genome ...

dqq20 commented 3 years ago

You can still remove the filtering of multiple hits (RM_MULTI=0) in the config, but be careful with the interpretation, as the reads aligned on this region can come from another homologuous region, elsewhere on the genome ...

OK, I will try it,thank you!