paired-end files with reads on different strand

Question

[tina.khajeh]

I want to align reads in 2 different files using paired-end alignment with the help of bowtie. when I try to align it with bowtie1 it fails and a little portion of it just align to the reference genome. I aligned each file separately as a single read and when checked 2 SAM output files I saw that the flag values for entries in first file and second file are 0 for some entries and 16 for others,which I think means that some reads for each file were on the + strand and others on - strand also when flag value for entry number N is 0 for first file it's corresponding flag value for N'th entry in second file is 16 . I want to know what should to do if I want to align it bowtie1? Is it true if I reverse all entries in first file and make all reads of first file on the same strand and do the same thing for second strand and then align it?

The other question is that bowtie2 can map these two files, how can I be sure that mapping is true?

Answer 1

[swbarnes2]

Don't reverse your reads, paired end reads are supposed to be on opposite strands. Bowtie is smart enough to know this. The first thing I'd try is changing the settings to tell it to expect a very large potential insert size between the reads; I think bowtie often refuses to report alignments if it thinks the reads are too far apart, and the default distance is very small.

[tina.khajeh]

Thanks, The problem solved :)

[Deepak Tanwar]

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