Visualization

Question: Visualization

7.1 years ago by

wu yijin • 10 wrote:

Hi All, I am new of Galaxy. I want to visualize my short mapping results in the browser. I uploaded my .wig file which has format as this, (first column is position, second is the read soverage of that position) variableStep chrom=Chr1 4 1 5 1 6 1 7 1 8 2 9 3 10 3 11 3 12 3 13 3 14 3 15 3 16 4 17 4 18 4 But it comes an error Couldn't open /galaxy/home/g2main/galaxy_main/tool- data/shared/ucsc/chrom/arabidopsis.len , No such file or directory Does anyone know how to fix this? Many thanks! Best, Peggy

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modified 6.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.1 years ago by wu yijin • 10

7.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Peggy, The reference genome named simply "arabidopsis" in Galaxy is a legacy genome name and may not work with all tools. Assigning the reference genome name "Arabidopsis_thaliana_TAIR9" instead is the recommended choice (both are TAIR9). The next item to change is the format of the chromosome names, specifically the capitalization. The file you loaded has chromosome names like "Chr" and in both the "arabidopsis" and "Arabidopsis_thaliana_TAIR9" genomes on the Galaxy main server, the chromosome names are like "chr". Reassigning the database and correcting the capitalization in the input file may resolve the issue. Another choice is to load the reference genome you used to generate the data into your history in fasta format, and use it as a custom genome for visualization. If you need help with any of this, please let us know, Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

ADD COMMENT • link written 7.1 years ago by Jennifer Hillman Jackson ♦ 25k

6.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Ateeq, The BAM/SAM files can be visualized in Trackster, using your custom reference genome (the same dataset as used for Bowtie or TopHat). But, there are no Cufflinks results, and therefore nothing to visualize, due to the parameters used. Since you are working with a bacterial genome, the parameters will need to be tuned to account for the lack of transcript splicing. The best resources for advice are likely seqanswers or the tool authors, as explained in this prior answer to another bacterial genome/RNA-seq question: http://galaxy-users-list-archive.2308625.n4.nabble.com/Cufflinks- merging-more-than-one-transcript-on-bacterial-genomes-td4323709.html Recently, there has been some user discussion about RNA-seq analysis and bacterial genomes on the galaxy-user mailing list. If you want to search and read through the Q&A, using our custom google search is the best way to locate the threads (but, expect to find just a few): http://galaxy.psu.edu/search/mailinglists/ If anyone else reading this thread has help to offer, please feel free to jump in and share any working knowledge for this type of analysis. Best wishes for your project, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

ADD COMMENT • link written 6.8 years ago by Jennifer Hillman Jackson ♦ 25k

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