Hi all,
I am trying out different ways to get summary statistics of how well my solexa reads have been aligned to my reference genome. Some aligners, eg bowtie, provide reasonable statistics of number of mapped reads, number of reads with x mismatches and so on but others don't. I would a like a way to, given a fastq file and a sam file, obtain such basic statistics.
Does anyone know of such a tool?
cheers
I am trying out different ways to get summary statistics of how well my solexa reads have been aligned to my reference genome. Some aligners, eg bowtie, provide reasonable statistics of number of mapped reads, number of reads with x mismatches and so on but others don't. I would a like a way to, given a fastq file and a sam file, obtain such basic statistics.
Does anyone know of such a tool?
cheers