 bash -c  /opt/chipster/tools/bowtie2/bowtie2 --sensitive --mp 6 --np 1 --rdg 5,3 --rfg 5,3 --phred33 --no-unal -x /opt/chipster/tools/bowtie2/indexes/hg19 -U reads1.fq
71650 reads; of these:
  71650 (100.00%) were unpaired; of these:
    12570 (17.54%) aligned 0 times
    49935 (69.69%) aligned exactly 1 time
    9145 (12.76%) aligned >1 times
82.46% overall alignment rate
total 40964
-rw-r--r-- 1 chipster chipster 28246312 2013-05-09 10:43 alignment.sam
-rw-r--r-- 1 chipster chipster      377 2013-05-09 10:43 bowtie2.log
-rw-r--r-- 1 chipster chipster        0 2013-05-09 10:42 bowtie2.log 
-rw-r--r-- 1 chipster chipster 13691272 2013-05-09 10:42 reads1.fq
