Hi all,
I have a question regarding what I though would be a simple thing to do, but cannot find an efficient method to implement it...
I have several individual alignments that were each assembled to the same annotated reference genome (large gaps in each as I targeted genes for sequencing), and I am trying to find a way to compare the various alignments to one another to see whether or not the same gene (or other) regions were recovered in each assembly (i.e. repeatability of my sequencing strategy). I don't care about minor differences (e.g. SNPs) between the individuals, just whether or not they 'hit' the same genomic region. It seems that the information is in the SAM/BAM file I have produced, but I can't seem to find an efficient way to extract and compare each region for all of the individuals.
Any help would be much appreciated.
I have a question regarding what I though would be a simple thing to do, but cannot find an efficient method to implement it...
I have several individual alignments that were each assembled to the same annotated reference genome (large gaps in each as I targeted genes for sequencing), and I am trying to find a way to compare the various alignments to one another to see whether or not the same gene (or other) regions were recovered in each assembly (i.e. repeatability of my sequencing strategy). I don't care about minor differences (e.g. SNPs) between the individuals, just whether or not they 'hit' the same genomic region. It seems that the information is in the SAM/BAM file I have produced, but I can't seem to find an efficient way to extract and compare each region for all of the individuals.
Any help would be much appreciated.
Comment