Paired End Tags in Bowtie2

[sameeranc]

Hello,

I am new to this field and this is the first time I am using Bowtie2. I installed Bowtie2 and created the index files for Hg19. (I tried a SET file and it maps without a problem)
I want to align a paired end tag data set. I downloaded the CTCF PET dataset from http://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR525042 and created the two fastq files using SRATools.

Then I used the following command in Bowtie2.

/home/Bowtie2/bowtie2-2.2.2/bowtie2 -x /home/Hg19/Reference/humanGenome -1 /scratch/PET/SRR525042_1.fastq -2 /scratch/PET/SRR525042_2.fastq -S CTCFFinal.sam

But I am getting almost zero map. I tried using --ff/--fr/--rf but no luck so far.
Any help would be appreciated. Thanks in advance.

[dpryan]

Try mapping them as single end and see where pairs map then (they should be close together, but perhaps they'll be far apart or in weird orientations, all of which can normally prevent mapping).

[Ohad]

I think this is your prolem:

-x /home/Hg19/Reference/humanGenome

Are your files named "humanGenome.1.rev.bt2 ..etc" ?

I think you should use:

-x /home/Hg19/Reference/humanGenome/hg19 if your files named hg19.1.rev.bt2