Sequence direction in alignment

[newbietonextgen]

I have a simple question. We use illumina reads for a RNA seq analysis. when i visualize the alignment using IGV, i see reads that are pointed in two orientations? I would expect the reads to be in the 5'->3' but find both 5 to 3 and 3 to 5 orientation. Why do i find the mix of sequences? Does such a mix limit the analysis?

Thanks

[swbarnes2]

There are strand-specific Illumina preps, but if the RNA is turned in to cDNA, strand info will be lost.

You can talk to whomever preps the RNA, but you data sounds like it came from a non-strand-conserving prep.