comparing alignments

[sooper]

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.

[moritzhess]

I do not know if this of great help, but if you are a little bit familiar with python (really just a little bit), the HTSEQ (http://www-huber.embl.de/users/ander.../overview.html) package could be of help. It delivers (in my opinion) very good and convenient methods to parse bam files and extract for instance the regions, where your reads aligned to. You can also very easily create .bed files that can be loaded into a genome browser. On the webpage you find a very good tutorial where the most common applications are explained in ready to use examples.