[galaxy-dev] Slice bam

[jean_jasinski]

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:

chr11   249250621
chr21   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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[galaxy-dev] Slice bam

[jean_jasinski]

I wanted to remove all the non-standard reads (reads from non-standard 
chromosomes) from a bam file.  I used Slice bam and the bed file contained all 
of the chromosome lengths for chr1-22, x, and y.  But all I get back in the bam 
file are the unaligned chromosomes.

What am I doing wrong?

Jean Jasinski



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