I have a dual transcriptome of a bacteria and its host, a plant. I identified a preliminar assembly of the reads and it matches with our bacteria (70%) and the plant (30%). After that, I used Bowtie2 in order to map the reads to the genome of the bacteria (the same strain) and to the genome of the plant (a public one). This approach let me to obtain only a 19% of the reads aligned to the genome of the bacteria and 1% of the reads aligned to the plant. Taking into account that there are not reads from other microbes, it is normal to obtain so low aligment? Should I use another approach? Thank you very much in advance
Bowtie2 uses non-gapped alignments and therefore won't map any plant reads reads that span introns. You need to use Tophat2 or STAR. Additionally, the low mapping efficiency to both genomes may be because you have adapter contamination in your reads, poor sequence quality, or significant sequence divergence between your reference and the strain from which the reads were derived.
I completely agree with Mark. You want to clean your sequences and use a spliced alignment tool. Try Hisat2 instead of Tophat2. It is way faster (an uses RAM more efficiently than STAR).
Consider using a splice-aware aligner, that is, an aligner that would not try to align your RNA-Seq reads to introns, but will rather try to identify downstream exons, and try to map reads to those exons. Additionally to the alignment tools mentioned above by Mark Farman and Katharina Jasmin Hoff , I'd also recommend HISAT2, if speed and memory are a concern.
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