I have binned the mouse genome into fragments based on restriction
enzyme cut sites.  So each bin is a fragment flanked by say BamHI.  The
output file is in the interval format: chr# start and end coordinates of
each bin.  I want to count how many times each bin has reads that align to
it.  I mapped my reads using bowtie and generated a dataset (interval
format) for the aligned reads.  I then used join in "operate on genomic
intervals" and asked it to return intervals that innerjoin the "bin file".
The subsequent steps involve grouping and counting and then joining back to
the 1st dataset (BamHI delimited bins).  I have tried this workflow on
small datasets and it worked.  However when I subject my full alignment
file and full BamHI delimited bin file, the tool fails.  I am doing this on
cloud.  Any advice would be appreciated!

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