Hi:
I have some 454 and sanger reads that I want to map to a genome. I've tried with gmap. gmap find the introns, but tends to do a lot of small misalignments inside the exons that end up as false positive SNPs.
I was wandering about possible alternatives. I've read the tophat page, but I don't know if it would be ok to map long reads (sanger and 454) with tophat. tophat is based on bowtie in the bowtie website the do not recommend to use it with long reads.
Any advice on this matter.
Best regards,
Jose Blanca
I have some 454 and sanger reads that I want to map to a genome. I've tried with gmap. gmap find the introns, but tends to do a lot of small misalignments inside the exons that end up as false positive SNPs.
I was wandering about possible alternatives. I've read the tophat page, but I don't know if it would be ok to map long reads (sanger and 454) with tophat. tophat is based on bowtie in the bowtie website the do not recommend to use it with long reads.
Any advice on this matter.
Best regards,
Jose Blanca
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