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Old 10-23-2013, 06:38 PM   #1
Junior Member
Location: USA

Join Date: Oct 2013
Posts: 9
Default Help with bowtie2 for a beginner (windows)

As I am completely new to the field of Next Generation Sequencing and I have absolutely no background in computers, I need your help in figuring out the mistakes that I am doing while conducting sequence alignment. I am using bowtie2. The command that I have entered is:

./bowtie2 -p 8 -x hg19 NA11881.fastq > Experiment1.sam

And the result that I get is:

0 reads
0.00% overall alignment rate

I know I am going wrong somewhere. Please help! Any links to help me solve this problem will be appreciated.

Thank you!
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