Hi all,
I've used BWA to map short reads to the yeast genome. The protocol is RIP-seq (RNA ChIPseq), the sample prep includes creating ds cDNA from the RNA and sequencing the cDNA, so the strand data is not preserved.
When looking at mapping in a genome viewer I noticed that transposons seem to have a strand bias in favor of the reverse strand! Other features in the genome didn't show this.
I guess this is some kind of bias due to mapping. Does anyone know what might cause this?
Thanks,
Rachelly.
I've used BWA to map short reads to the yeast genome. The protocol is RIP-seq (RNA ChIPseq), the sample prep includes creating ds cDNA from the RNA and sequencing the cDNA, so the strand data is not preserved.
When looking at mapping in a genome viewer I noticed that transposons seem to have a strand bias in favor of the reverse strand! Other features in the genome didn't show this.
I guess this is some kind of bias due to mapping. Does anyone know what might cause this?
Thanks,
Rachelly.
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