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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
