It seems like Slice_bam should be pretty straight-forward to use, but when I 
run it and give it a bed file that contains the human chromosomes with their 
lengths like this:

chr1    1       249250621
chr2            1       243199373
for all chromosomes 1-22, X, Y.

I don't get the reads on chr1 and 2; instead, all I am left with are the reads 
on the nonstandard chromosomes (the unmapped scaffolds).

Any idea what I am doing wrong?

Jean Jasinski

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