Hi all, I am trying to use BOWTIE to do alignment for chipseq data. I need to provide one parameter named "fraction of human genome mappable by reads". The default is 80%. Is this a good default parameter for hg18?
In addition, I found the genome size statistics from the following web: http://genomewiki.ucsc.edu/index.php/Genome_size_statistics It says that, for hg18, the total size is 3,107,677,273 and called bases in the assembly is 2,881,421,696. Can I do the following simple calculation: 2,881,421,696/3,107,677,273 = 92.7%, and claim that "fraction of human genome mappable by reads = 92.7%"? Thanks for your attention. I will be looking forward to your kind reply. Best wishes, Shuying _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
