Solid RNA-seq pair end alignment read orientation

Question

[ewre]

Hi all,

Recently I have mapped a SOLiD 5500xl pair end sequencing data to reference transcripts. Only uniquely mapped reads are retained. after imported to integrative 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?

Many thanks.

Answer 1

[Brian Bushnell]

Solid reads are inward-facing, just like Illumina reads. If you found some document that states otherwise, it's incorrect.