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MAPS with Squirrel Genome #46

Open Elliott77 opened 2 years ago

Elliott77 commented 2 years ago

I've successfully defined significant interactions in mouse PLAC-seq data with your excellent MAPS pipeline. Thank you so much for sharing this. I'd now like to use MAPS with PLAC-seq data from 13-lined ground squirrel. I've altered, I think, the code in feather_split_rongxin.py to accommodate the squirrel scaffold names (see below), but I need a features file for the squirrel genome. Do you have code you could share for making a features file for another genome at 5 and 10kb resolution?

Thanks so much!

Elliott

altered feather_split_rongxin.py:

these are the scaffolds that correspond to the mouse X chromosome.

    chrX_scaffold = ["JH393524.1", "JH393493.1", "JH393302.1", "JH393309.1", "JH393629.1", "JH393705.1", "JH393596.1", "JH393289.1", "JH393619.1", "JH393299.1", "JH393336.1", "JH393737.1", "JH393561.1", "JH393357.1", "JH393851.1", "JH393384.1", "JH393459.1", "JH393573.1", "JH393555.1", "JH393394.1", "JH393623.1", "JH393434.1", "JH393719.1", "JH393283.1", "JH393375.1", "JH393531.1", "JH393880.1", "JH393501.1", "JH393326.1", "JH393654.1", "JH393296.1", "JH393323.1", "JH393359.1", "JH393284.1", "JH393543.1", "JH393280.1", "JH393388.1", "JH393454.1", "JH393312.1", "JH393492.1", "JH393285.1", "JH393507.1", "JH393363.1", "JH393963.1", "JH393324.1", "JH393646.1", "JH393412.1", "JH393303.1", "JH393319.1", "JH393790.1", "JH393445.1", "JH393317.1", "JH393909.1", "JH393362.1", "JH393500.1", "JH393587.1", "JH393572.1", "JH393298.1", "JH393399.1", "JH393769.1"]

autosomal_chrs = [chr_name for chr_name in chr_list if ((chrname.find('') == -1 and chr_name.find('.') == -1 and chr_name[3].isdigit()) or chr_name == "chrX" or chr_name == "chrY")]

    autosomal_chrs = [chr_name for chr_name in chr_list if (chr_name in chrX_scaffold)]

    potential_chrs = chr_list ##
    autosomal_chrs = [x for x in autosomal_chrs if x in potential_chrs]
    chr_list = autosomal_chrs