Hello Bioinformatic community,
We have recently sequenced a bacterial transcriptome with 316 chip from IonTorrent (1.5 million sequences). After filtering low quality data and trimming adapters we noticed that only 51.33% sequences were mapped on reference genome. Looking for the unmapped sequences we can see that most of them are chimeric transcripts, so impossible mapping for them an also causing bias on results. Also many of the unmapped are sequences lacking homology in 20% of the starting sequence.
I would like to know your opinion about it.
Should I have to move to 454 or Illumina? Our Sequencing Department have no idea of why we have so many chimeras.
Thank you, Bernardo
We have recently sequenced a bacterial transcriptome with 316 chip from IonTorrent (1.5 million sequences). After filtering low quality data and trimming adapters we noticed that only 51.33% sequences were mapped on reference genome. Looking for the unmapped sequences we can see that most of them are chimeric transcripts, so impossible mapping for them an also causing bias on results. Also many of the unmapped are sequences lacking homology in 20% of the starting sequence.
I would like to know your opinion about it.
Should I have to move to 454 or Illumina? Our Sequencing Department have no idea of why we have so many chimeras.
Thank you, Bernardo
Comment