Stitch Maf Blocks

Question: Stitch Maf Blocks

5.2 years ago by

Hi, I don't undestand how to use the tool "Stitch MAF blocks". I update a small bed file and now I need to run this tool, I don't understand the next step. I'm searching for Novel Linc in some RNA-seq data and I found the lncRscan tool (http://code.google.com/p/lncrscan/wiki/example) and now I have to use "Stitch MAF blocks". The point is: I update the bed file, I select Fetch Alignments -> Stitch MAF blocks, and then I can do nothing, I can only choose among "locally cached alignments" and "alignments in your history". But MAF type/MAF file remain empty, in any case. Can someone be so gentle to solve my problem? Do I need to download a MAF file? Is it normally on Galaxy server, but now it is down? How can I produce a MAF file selecting only some species (29 mammals)? Thank you really much. Jennifer

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modified 21 months ago by biofilia • 0 • written 5.2 years ago by Jennifer Di Tommaso • 20

5.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello, Yes, this tool functions on MAF input. For examples through several cases with this tool group, including this tool, please see: " Making whole genome alignments usable for biologists" publication & supplemental. https://main.g2.bx.psu.edu/u/dan/p/maf "Using Galaxy" publication & supplemental. Protocol #5 https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012 The public Main server is experiencing some performance issues right now, so please give it some time before trying out the exercises & your analysis. Reviewing the pages should be fine. Screencasts can be watched on any browser except Firefox (use Chrome, Safari) Thanks, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD COMMENT • link written 5.2 years ago by Jennifer Hillman Jackson ♦ 25k

Hi, thanks for the answer. I understand my problem: I'm using mm10 and the alignment is avaible only for mm9, is it possible for you to fix it? Thanks. Jennifer ________________________________ Da: Jennifer Jackson <jen@bx.psu.edu> Inviato: marted? 24 settembre 2013 17:13 A: Jennifer Di Tommaso Cc: galaxy-user@lists.bx.psu.edu Oggetto: Re: [galaxy-user] Stitch MAF blocks Hello, Yes, this tool functions on MAF input. For examples through several cases with this tool group, including this tool, please see: " Making whole genome alignments usable for biologists" publication & supplemental. https://main.g2.bx.psu.edu/u/dan/p/maf "Using Galaxy" publication & supplemental. Protocol #5 https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012 The public Main server is experiencing some performance issues right now, so please give it some time before trying out the exercises & your analysis. Reviewing the pages should be fine. Screencasts can be watched on any browser except Firefox (use Chrome, Safari) Thanks, Jen Galaxy team Hi, I don't undestand how to use the tool "Stitch MAF blocks". I update a small bed file and now I need to run this tool, I don't understand the next step. I'm searching for Novel Linc in some RNA-seq data and I found the lncRscan tool (http://code.google.com/p/lncrscan/wiki/example) and now I have to use "Stitch MAF blocks". The point is: I update the bed file, I select Fetch Alignments -> Stitch MAF blocks, and then I can do nothing, I can only choose among "locally cached alignments" and "alignments in your history". But MAF type/MAF file remain empty, in any case. Can someone be so gentle to solve my problem? Do I need to download a MAF file? Is it normally on Galaxy server, but now it is down? How can I produce a MAF file selecting only some species (29 mammals)? Thank you really much. Jennifer ___________________________________________________________ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD REPLY • link written 5.2 years ago by Jennifer Di Tommaso • 20

Hello Jennifer, Yes, only hg19 and mm9 are locally cashed for the MAF tools. However, you can also load MAF data and use that from the history with these tools. The best way to do this is to load data by chromosome from UCSC: http://hgdownload.cse.ucsc.edu/goldenPath/mm10/multiz60way/ the "/maf" directory contains data If you find that you need more compute or space, then a local or cloud Galaxy is recommended. Please also note that due to our current infrastructure changes, (updates will be in the banner on the public site), data transfer and jobs may have longer delays that usual during the next few weeks, until the transition is complete. Hopefully this helps, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD REPLY • link written 5.2 years ago by Jennifer Hillman Jackson ♦ 25k

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