paired end mapping using bowtie

[mansoorhasani]

Hi all
I'm really nub to working with bowtie. I have two fq files that contained paired end reads for a child . The files are child1-1.fq and child1-2.fq and I have a reference file with the name of ref.fa . I want use bowtie to map this paired end read to the reference seq and I'm using the following command but the output wasn't good. I think that I don't use correct option like -I and -X . actually I don't what should I select for those options .
any suggestion will be nice.
thanks you all.
my command is:

bowtie-build  ref.fa ref_index
bowtie -v 2 -S ref_index -1 child1-1.fq -2 child1-2.fq > child1_align.sam

and the output is :

# reads processed: 25000
# reads with at least one reported alignment: 16 (0.06%)
# reads that failed to align: 24984 (99.94%)
Reported 16 paired-end alignments to 1 output stream(s)

some lines of child1-1.fq:

@child_1192360_1192917_1:0:0_1:0:0_2dc6c/1
GGACTTTGAGCTCGGGATGAATGTGCCTGCTGACTTTGCTGTTGCCTCTGTTGTAATCTATTATTCACTG
+
2222222222222222222222222222222222222222222222222222222222222222222222
@child_652211_652627_0:0:0_2:0:0_2dc6d/1
TTTTTATGAGCTCATGTTATAAATACAGATAAGACAGAATTGAGAACGAGGAGAAAGAGCGATCTATGCG
+
2222222222222222222222222222222222222222222222222222222222222222222222

and some lines of child1-2.fq:

@child_1192360_1192917_1:0:0_1:0:0_2dc6c/2
GGAACTGGTCAAAAATATTAACACATATGGCTACACTTGGGAATTGATTAGTGCACATATGACACATCGC
+
2222222222222222222222222222222222222222222222222222222222222222222222
@child_652211_652627_0:0:0_2:0:0_2dc6d/2
ACTAAGATTTCATTCCAACACTACATTTTTTCGGAAAACGTTTTATTGAAGTACTGCTTTATGGTCAGCA
+
2222222222222222222222222222222222222222222222222222222222222222222222

[Brian Bushnell]

It looks like you have contamination. Running these through BLAST indicates they are from Saccharomyces cerevisiae, not human. So, you won't be able to map them to a human reference.

[mansoorhasani]

It looks like you have contamination. Running these through BLAST indicates they are from Saccharomyces cerevisiae, not human. So, you won't be able to map them to a human reference.

thank you, my problem was solved by using bowtie2