Hi Nate, When I operate on Genomic Intervals → Get Flanks. The user interface for the tool will appear in the center panel. Make sure the dataset 2: UCSC Main... is selected and set Length of Flanking region to 1000 to create intervals 1000bp upstream of each gene. I have this error : Tool execution generated the following error message: WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched The tool produced the following additional output: Skipped 2 invalid lines starting with #40094L "chr5_h2_hap1 281 935 NM_022909 0 + 281 377 0 1 654, 0," Location: Upstream, Region: whole, Flank-length: 1000, Offset: 0 Epilog : job finished at ven avr 6 13:59:08 CEST 2012 Moreover, when I Map with BWA for Illumina ( genome ref and fastq fatsqsanger format ), I have this error : Tool execution generated the following error message: entree dans bwa wapperThe alignment failed. Error aligning sequence. /bin/sh: bwa: command not found WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched The tool produced the following additional output: entree dans bwa for illumina Could not determine BWA version Epilog : job finished at ven avr 6 14:04:13 CEST 2012 Could you please help me ? Thanks in advance, Sarah Maman