Hello, <br>        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 &quot;operate on genomic intervals&quot; and asked it to return intervals that innerjoin the &quot;bin file&quot;.  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!<br>
<br>Jose<br>