Re: [galaxy-user] Questions regarding Circster visualization
1. I tested it using a bigWig and a BED file. Both were loaded nicely in Circos, but I was surprised to see that the visualization of both files looked exactly the same, i.e. both file types seemed to be interpreted as histograms/coverage data. From the Circos plots I've seen in publications, I assumed that BED files should be visualized as straight lines, indicating genome regions (rather than a coverage). Am I doing anything wrong? Or, rather, how should I modify the BED file so that its content is simply interpreted as genomic regions? This is a limitation of the visualization, and it should be addressed. I've created a Trello card for this enhancement that you follow here: https://trello.com/c/YIdx6QvV 2. In the Galaxy publication (www.biomedcentral.com/1471-2164/14/397), line data is mentioned for displaying connecting lines in the center of the circle - could you give me an example line of how this kind of data needs to be formatted? The format is a 7-column tabular file with tab-separated values: -- chrom1 start1 end1 chrom2 start2 end2 score -- Score isn't used right now, but it still needs to be there. Once you have this format, you'll need to convert the datatype from 'tabular' to 'chrint' in order to visualize it (click on the pencil icon -- Datatype. Also, I have a workflow up to convert Tophat fusion output data to chrint format here: https://usegalaxy.org/u/jeremy/w/tophat-fusion-post-output-to-chrint Sorry for the cryptic nature of everything right now. We'll get this info and more up on a wiki page eventually (you're welcome to start one in the meantime). Let us know if you have more questions. Best, J. ___ 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/
Re: [galaxy-user] Help with Cuffdiff
Hi Maria, I didn't notice any obvious problematic usage, format, or content issues with the Tuxedo pipeline execution in your history. Your protocol is right on track. This leaves data and parameter inputs to consider. I did notice that you are mainly using defaults and omitting the use of reference annotation that Cuffdiff uses to generate the full compliment of statistics. The NOTEST result indicates that the coverage is too shallow. You could follow the advice here, by adjusting -c to be lower. This is Min Alignment Count: and is set to 10 in your runs. http://cufflinks.cbcb.umd.edu/faq.html#notest Adding in a reference annotation file could also potentially help. Aligned sequences may be falsely fragmenting without a reference transcript to help bind them together. But, this is just a guess - I didn't examine any assembly regions. This is however something that you could do. The UCSC Table Browser is one source for a GTF file. Experimenting with other parameters as you are doing also is worth it. The manual and such cover these in detail, and there is always the tool author's google group for detailed questions/advice. Good luck with your project, Jen Galaxy team On 2/6/14 12:38 PM, Maria Hoffman wrote: Hello, Thank you for your help. I have found that wiki page very helpful and actually us it very often (I was using it this AM too before I emailed you). In looking at the wiki again, nothing is really standing out to me ( my chromosome notation matches up etc). I am going to keep looking etc but I did send you my history too. I did try running another cuffdiff playing with the dispersion estimation method too out of curiosity. Thank you so much for your help! This is my first real data set doing this and we have abstracts due soon, so the pressure is on! Thanks! Maria -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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/
