Dear Galaxy user:
Below are two important points about Galaxy genome builds that may affect your analysis results:
1. Canonical and Complete builds
Many genomes provided by Galaxy originate from UCSC and are represented by a mix of canonical chromosomes (such as 1 through Y in mammals), mitochontrial genome (chrM), and unplaced fragments (chrUn) and/or haploblocks. Until last week we were using only canonical chromosomes and the mitochondrion to build indices required by NGS mappers (bwa, bowtie, bfast, lastz, and perm) and SAM Tools. However, for some analyses it is necessary to include regions that are not placed within the canonical chromosome set. Starting next week we will be providing two sets of NGS mapper indices: canonical (chr1 through chrY + chrM) and full (everything). A separate message will be sent out once this is enabled.
2. A recent un-announced change to hg19
The hg19 version of NGS and SAMTools indices contained only CANONICAL chromosomes (chr1 through Y + chrM) until August 20. On August 20 it was changed to the full version. As a result mapping jobs that were run after August 20, 2010 may return slightly different results.
Anton Nekrutenko http://usegalaxy.org