Monday, January 26, 2015

Remember to sort when using bedtools groupby!

Learned this the hard way. At the very end of the bedtools groupby help message, in the notes section, it says: "The input file/stream should be sorted/grouped by the -grp. columns". AUGH. Note that this is absolutely NOT a constraint posed by SQL's group by, even if their bold claim of 'Akin to the SQL "group by" command' may lead you believe otherwise. Talk about false advertising!

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