[galaxy-user] GATK tools: other genome available?
Hi, The NGS: GATK Tools on main are so far only for human genome. Do you have an idea when other genomes (such as my favorite, i.e mice and mm9) would be accessible ? Otherwise, is there a way to easily transfer mm9 genome that is system-installed on main directly in a Custom build genome that could be used in such a case ? Or is this a bad idea ? Thanks for your help, Best. Jean Jaubert ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Mapping paired end reads with Tophat
Hi all, After mapping, I used IGV to have a look at the mapping. There are a lot of mapped reads without pair reads. Should I keep these reads? or Is this a problem for cufflinks analysis? What I tried is: 1. BAM to SAM 2. Filter SAM: set Read mapped in a proper pair to Yes. The result is that only 1/5 reads were left. Can anybody tell me if this operation is proper?? How do you normally optimize the mapping rerults from Tophat? Which considerations should I take into account? Looking forward to your reply. Jiwen ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
