bowtie paired end mode

[boetsie]

hi all,

i want to use bowtie for sort of paired end alignment, when i do;

bowtie.exe TESTTT -c CACCGAAAGACA,AGTAGCCACGGCGCAGCAACAC

it works fine, and i get two outputs.

However, when i do them in paired end mode;

bowtie.exe TESTTT -1 file1.txt -2 file2.txt

it doesn't work, since it generates no outputs. Someone knows how to generate such a file? Can it be a .fasta file?

Cheers,
Marten

[adamdeluca]

http://bowtie-bio.sourceforge.net/manual.shtml

-f specifies fasta, by default fastq is assumed