juicer

[ningwei-wei]

hi yufanzhou your method is very useful . but i have a little question. the juicer's result, like "resule.hic", whether it can be deal with HiSIF. if it can , how shou i do ?

i will appreciate if you can replay me quickly

[yufanzhouonline]

Hi Ningwei, Please refer to hicConvertFormat: https://hicexplorer.readthedocs.io/en/latest/content/tools/hicConvertFormat.html If you want to transfer pairs to .hic then refer to Juicebox Pre: https://github.com/aidenlab/juicer/wiki/Pre

After you get the pairs, just transfer them to the following 6-column text file:

chr1 pos1 strand1 chr2 pos2 strand2

chr1/chr2 are chromosomes, pos1/pos2 are mapped genomic loci. Please note strand is 1 for positive strand and 0 for negative strand. Each chromosome need only the number and chrX is 23 and chrY is 24. That means chr1/chr2 must be 1-24.

Thanks.

[kuangzhuoran]

老师您好！ 我不是很理解 "following 6-column text file: " 是一种怎样的文件格式 juicer或者HiC-Pro输出的互作格式，都是类似的: Chr1 0 100000 Chr1 100000 200000 12.3 染色体1 起始bp 终止bp 染色体2 起始bp 终止bp 互作强度

有两个问题想请教一下老师 1.老师您说的pos1/pos，是起始bp还是终止bp 2.strand的信息在juicer或者HiC-Pro中好像并没有

[yufanzhouonline]

Hi Kuangzhuoran,

1. Start bp
2. They contain strand information, please read their documents. Thanks.

[kuangzhuoran]

Thanks for your reply！Sorry to interrupt again

I found that the output of the straw or juicer_tools dump (juicer pipeline) did not have that

As for hicConvertFormat, "--outputFormat {cool,h5,homer,ginteractions,mcool,hicpro}", I have tried all outputFormats, but they are all binary

I don't know what to do now = =

[yufanzhouonline]

Hi kuangzhuoran,

On this page https://github.com/aidenlab/juicer/wiki/Pre, the .hic file format is clearly described.

[kuangzhuoran]

Thanks ~ I'm still confused.

Juicer pre is used to create a .hic file and the required input format contains strand information. The .hic file that I get from the juicer pipeline will no doubt contain strand information as well.

How do I extract the strand information; both the ‘juicer dump’ and ‘straw.py’ only get three columns of information: pos1 pos2 score

HiC-Pro outputs a matrix file with similar three columns: pos1 pos2 score I have not found a way to extract the strand information from HiC-Pro's output file yet = =

[yufanzhouonline]

Hi kuangzhuoran,

Please ask the authors of Juicer or HiC-Pro if you have any questions about their outputs, thanks.

If you just only want to get strands in specific loci you can extract this information from annotation of reference genome which you are using. Maybe you need to ask somebody or google search about the topic of genomic annotation. Thanks.

[kuangzhuoran]

Thanks a lot ! I get it