Make Blastn search with paired end reads

[Guest]

Hi all,

I have a problem to align paired ends read with blastn app to the hg 19.
My reads stored in F3 and F5_P2 files. They are 50 and 35 bp long, and there are millions read in a file. My goal is that to align them into the human genom 19, but i don't have any idea how to do this.
I make the blast db for the hg19, and i run blastn with one input (i try with the F3 and F5_P2 as well), but thats not what i wanted to do. I want to map both files at the same time. I read the blast cmd manual, and the blastn help, but i don't seen any reference to map paired end reads.
In seqanswer forum i don't found any thread that might help me.
My inputs are in fasta format.

Does anybody have idea, how to solve my problem?

Sorry for my poor english!
Thanks

István

[mastal]

what you want is a short read aligner, like BFast if you have SOLiD data, or Bowtie or BWA.

see the link below for more info:

http://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Alignment

[Guest]

First of all, thank you mastal, for your reply

I'm know the bowtie software, and i used it, but my real goal is that, to using somehow the blastn to map the hg19 with my paired end reads.

Is there any way to append my paired end reads in a file correctly to get an accepted input for the blastn?