I have a Trinity assembly for a eukaryotic transcriptome (default parameters) and Illumina PE genomic shotgun reads (unassembled). I want to verify that the results of my assembly exist in my genome.
I have been blasting particular transcripts against the genomic reads, pulling out the reads and aligning them back to the transcript to look at coverage and verify whether there is assembly error. This is taking a long time and is not general enough for me to apply to 3 other transcriptome-assembly-genome-reads comparisons I would like to do.
Suggestions for methods to try?
I was thinking of using Exonerate to align genome reads back to transcriptome, but I'm not sure if that will take into account intronic sequences that are present in my genomic reads but not in the "reference" (the transcriptome assembly).
I have been blasting particular transcripts against the genomic reads, pulling out the reads and aligning them back to the transcript to look at coverage and verify whether there is assembly error. This is taking a long time and is not general enough for me to apply to 3 other transcriptome-assembly-genome-reads comparisons I would like to do.
Suggestions for methods to try?
I was thinking of using Exonerate to align genome reads back to transcriptome, but I'm not sure if that will take into account intronic sequences that are present in my genomic reads but not in the "reference" (the transcriptome assembly).
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