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Hi everybody,
I'm analyzing RNAseq data (from Solid, single end, 35nt, srek kit) to discover DE genes. Before starting the DE analysis I always separate reads aligning to the + strand from reads aligning to the - strand. Then I count the number of reads matching all exons. Although Solid sequencing claims to be strand specific I often find reads aligning to the opposite strand within exons. It is far to much for anti-sense transcription. Does anybody have comparable experiences and or an explanation? Thanks in advance.
Marcel
I'm analyzing RNAseq data (from Solid, single end, 35nt, srek kit) to discover DE genes. Before starting the DE analysis I always separate reads aligning to the + strand from reads aligning to the - strand. Then I count the number of reads matching all exons. Although Solid sequencing claims to be strand specific I often find reads aligning to the opposite strand within exons. It is far to much for anti-sense transcription. Does anybody have comparable experiences and or an explanation? Thanks in advance.
Marcel