recently I have mapped a SOLiD 5500xl pair end sequencing data to reference transcripts. Only uniquely mapped reads are retained. after imported to intergretive genome viewer, I found that the read orientation is un-identical to the IGV doucumentation which says that for SOLiD data, it is normal when two reads of a spot head to the same direction. my result shows that the reads are all pointed to each other(like normal ones for illumina data).
I use bfast+bwa for reads mapping.
How should I interpret this?