 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
84812 reads; of these:
  84812 (100.00%) were unpaired; of these:
    14247 (16.80%) aligned 0 times
    54797 (64.61%) aligned exactly 1 time
    15768 (18.59%) aligned >1 times
83.20% overall alignment rate
total 51572
-rw-r--r-- 1 chipster chipster 35496481 2013-05-09 09:56 alignment.sam
-rw-r--r-- 1 chipster chipster      378 2013-05-09 09:56 bowtie2.log
-rw-r--r-- 1 chipster chipster        0 2013-05-09 09:55 bowtie2.log 
-rw-r--r-- 1 chipster chipster 17304364 2013-05-09 09:55 reads1.fq
