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Hi guys,
I am having trouble with the mapping-to-genome process. I have a dataset of illumine reads. I have filtered them accordingly. In generating this dataset, we included some canine genes. I have mapped the short canine reads to the dog genome using bowtie to determine how many of the reads are useful. I have since assembled the reads into larger contgs of ~400bp. I now want to determine the quality of these contigs. Is it better to use blast to 'map' these large contains to the canine genome or to attempt to map them using bwa, bowtie, novoalign or some other type of mapping algorithm? What is the general rules of mapping?
Thank you!
I am having trouble with the mapping-to-genome process. I have a dataset of illumine reads. I have filtered them accordingly. In generating this dataset, we included some canine genes. I have mapped the short canine reads to the dog genome using bowtie to determine how many of the reads are useful. I have since assembled the reads into larger contgs of ~400bp. I now want to determine the quality of these contigs. Is it better to use blast to 'map' these large contains to the canine genome or to attempt to map them using bwa, bowtie, novoalign or some other type of mapping algorithm? What is the general rules of mapping?
Thank you!
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