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?
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