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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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High Filtered_pairs rate #513

Open zhanglp996 opened 2 years ago

zhanglp996 commented 2 years ago

Hello! I meet some troubles in running HiC-Pro.The Filtered_pairs rate in my Hi-C data is up to 40.8%.I check the allValidPairs and bwt2pairs.FilterPairs file but found no difference.What can I do to reduce the Filtered_pairs.

############################################################# GENOME_FRAGMENT = /30t/zhanglp/hic/bowtie2_index/genome_HaeIII.bed LIGATION_SITE = GGCCGGCC MIN_FRAG_SIZE = 100 MAX_FRAG_SIZE = 100000 MIN_INSERT_SIZE = 100 MAX_INSERT_SIZE = 1000

fafuyyk commented 2 years ago

Hello, have you found the cause of the problem, I also encountered a similar problem, my filtered pair is up to 60%

zhanglp996 commented 2 years ago

I also meet the problem. The Filtered_pairs rate  is associate to fragement size and insert size in hicpro, you could set the "MIN_FRAG_SIZE= " to resolve the problem. 

------------------ 原始邮件 ------------------ 发件人: "nservant/HiC-Pro" @.>; 发送时间: 2022年5月25日(星期三) 下午5:10 @.>; @.**@.>; 主题: Re: [nservant/HiC-Pro] High Filtered_pairs rate (Issue #513)

Hello, have you found the cause of the problem, I also encountered a similar problem, my filtered pair is up to 60%

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