Bowtie alignment for PE SOLiD data

Question

[nikkihathi]

Sorry my mistake: solution of simple:

bowtie -t -p 4 -C --sam Genome/mouce_database_10/mm10_c  -f -1 /SOLiD_data/F3/reads/5500xl_F3.csfasta -2 /SOLiD_data/F5-RNA/reads/5500xl_F5-RNA.csfasta --Q1 /SOLiD_data/F3/reads/5500xl_F3.QV.qual --Q2 /SOLiD_data/F5-RNA/reads/5500xl_F5-RNA.QV.qual  output1.sam 2> stdout.err

I think the question to use Bowtie to align PE SOLiD data should be easy, however, I cannot understand the error.

To perform PE alignment I am using the following code:

bowtie -t -p 4 -C --sam Genome/mouce_database_10/mm10_c  -f -1 /SOLiD_data/F3/reads/5500xl_F3.csfasta -2 /SOLiD_data/F5-RNA/reads/5500xl_F5-RNA.csfasta -Q1 /SOLiD_data/F3/reads/5500xl_F3.QV.qual -Q2 /SOLiD_data/F5-RNA/reads/5500xl_F5-RNA.QV.qual  output1.sam 2> stdout.err