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juicer #1
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Hi Ningwei, 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. |
老师您好! 有两个问题想请教一下老师 |
Hi Kuangzhuoran,
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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 = = |
Hi kuangzhuoran, On this page https://github.com/aidenlab/juicer/wiki/Pre, the .hic file format is clearly described. |
Thanks ~ I'm still confused. Juicer pre is used to create a .hic file and the required input format contains strand information. How do I extract the strand information; HiC-Pro outputs a matrix file with similar three columns: pos1 pos2 score |
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. |
Thanks a lot ! I get it |
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
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