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hi Seqanswer,
We have transcriptome data assembled using de-novo assembly approach. Recently, we have genome sequence available, therefore we decided to map the assembled transcripts to genome sequence, planing to look into splice junction and gene families. I came across with exonerate (http://www.ebi.ac.uk/~guy/exonerate/), which map the transcripts to the genome pretty well (using est2genome as alignment model).
Now here comes the challenge. Each transcripts consist multiple hits. Tried to filter according to score but doesn't work well. Any suggestion how to remove low quality hits but at the same time retain some good hits.
Anybody with this kind of experience before? Care to share with us?
Thanks is advance
We have transcriptome data assembled using de-novo assembly approach. Recently, we have genome sequence available, therefore we decided to map the assembled transcripts to genome sequence, planing to look into splice junction and gene families. I came across with exonerate (http://www.ebi.ac.uk/~guy/exonerate/), which map the transcripts to the genome pretty well (using est2genome as alignment model).
Now here comes the challenge. Each transcripts consist multiple hits. Tried to filter according to score but doesn't work well. Any suggestion how to remove low quality hits but at the same time retain some good hits.
Anybody with this kind of experience before? Care to share with us?
Thanks is advance