Visualization Of Alignment

Question: Visualization Of Alignment

7.3 years ago by

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Tao, For the Bowtie results, the aligned results may be low because the data is RNA and not DNA. TopHat is generally considered a better choice for RNA since it allows for bridges over splice sites (introns). The full documentation for each program is on each tool's form and/or you can contact the tool authors with scientific questions at tophat.cufflinks@gmail.com. Also, a tutorial and FAQ are available here: http://usegalaxy.org/u/jeremy/p/galaxy-rna-seq-analysis-exercise http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq For visualization, an update that allows the use of a user-specified fasta reference genome is coming out very soon. For now, you can view annotation by creating a custom genome build, but the actual reference will be not included. Use "Visualization -> New Track Browser" and follow the instructions for "Is the build not listed here? Add a Custom Build". Help for using the tool is available here: http://galaxyproject.org/Learn/Visualization As stated before, please email the mailing list directly and not individual team members. Specifically, with a "to" to the mailing list (only) and not including team members as a "to" or "cc" unless ask to do so when sharing private data. Our internal tracking system and public archives rely on this method. Thank you for your future corporation. Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

rna-seq alignment bowtie cufflinks • 814 views

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modified 7.3 years ago by Peng, Tao • 170 • written 7.3 years ago by Jennifer Hillman Jackson ♦ 25k

7.3 years ago by

Peng, Tao • 170

Peng, Tao • 170 wrote:

Hi Jen, I have been using the following link for learning to visualize TOPHAT results: http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise How can get the RefGENE for the whole human genome instead of Ch19 listed in tutorial? Thanks, tao To: galaxy-user@bx.psu.edu Cc: Peng, Tao Subject: visualization of alignment Hello Tao, For the Bowtie results, the aligned results may be low because the data is RNA and not DNA. TopHat is generally considered a better choice for RNA since it allows for bridges over splice sites (introns). The full documentation for each program is on each tool's form and/or you can contact the tool authors with scientific questions at tophat.cufflinks@gmail.com. Also, a tutorial and FAQ are available here: http://usegalaxy.org/u/jeremy/p/galaxy-rna-seq-analysis-exercise http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq For visualization, an update that allows the use of a user-specified fasta reference genome is coming out very soon. For now, you can view annotation by creating a custom genome build, but the actual reference will be not included. Use "Visualization -> New Track Browser" and follow the instructions for "Is the build not listed here? Add a Custom Build". Help for using the tool is available here: http://galaxyproject.org/Learn/Visualization As stated before, please email the mailing list directly and not individual team members. Specifically, with a "to" to the mailing list (only) and not including team members as a "to" or "cc" unless ask to do so when sharing private data. Our internal tracking system and public archives rely on this method. Thank you for your future corporation. Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

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