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Hi Folks
I'm mapping single read colourspace reads from a plant transcriptome analysis to EST data. We don't have a genome, so EST data is what we have to map against. I've used Bowtie to create an index with the EST data and mapped about 20% of the reads to the ESTs with default error mapping settings. I also tried mapping the reads against other plant genomes but we are seeing pretty low mapping of the reads onto these other genomes (around 10%).
I have tried mapping the reads with TopHat against the EST library as well but this errors out. Probably due the ESTs not being chromosomes, so intron/exon boundaries are not present, but I would be happy to be corrected on this point.
Is there any other strategy or software I should be using that would allow me to more efficiently map these reads?
Thanks for your time and replies.
I'm mapping single read colourspace reads from a plant transcriptome analysis to EST data. We don't have a genome, so EST data is what we have to map against. I've used Bowtie to create an index with the EST data and mapped about 20% of the reads to the ESTs with default error mapping settings. I also tried mapping the reads against other plant genomes but we are seeing pretty low mapping of the reads onto these other genomes (around 10%).
I have tried mapping the reads with TopHat against the EST library as well but this errors out. Probably due the ESTs not being chromosomes, so intron/exon boundaries are not present, but I would be happy to be corrected on this point.
Is there any other strategy or software I should be using that would allow me to more efficiently map these reads?
Thanks for your time and replies.