Solid RNA-seq pair end alignment read orientation
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6.3 years ago
ewre ▴ 240

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 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?

many thanks.

 

RNA-Seq SOLiD orientation • 1.7k views
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Entering edit mode
6.3 years ago

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

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