Map With Bowtie

Question: Map With Bowtie

7.6 years ago by

Sher, Falak • 80 wrote:

Hi Colleagues, I mapped illumina sequences using Bowtie on Galaxy server, I could not locate the information, like how many there were total reads and in what percentage they are mapped with mouse genome etc (samples were from mouse). Help and suggestions are greatly acknowledged, Thank you for attention, Falak

alignment bowtie • 1.0k views

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modified 6.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.6 years ago by Sher, Falak • 80

7.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Falak, The tools in "Text Manipulation", "Filter and Sort", and "Join, Subtract and Group" are designed to help with this type of file analysis (basic stats). Please explore and let us know if you need help with any particular tool, Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD COMMENT • link written 7.6 years ago by Jennifer Hillman Jackson ♦ 25k

Hello Falak, There may be another issue regarding metadata display we would like to confirm. Would you have time to share a link to your history? Options -> Share or Publish. You can send the link directly to me. Please note which dataset is the Bowtie result in question, if there are multiple in your history. Thanks! Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD REPLY • link written 7.6 years ago by Jennifer Hillman Jackson ♦ 25k

6.0 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Andrew, When a job is waiting to run, that means it is in the queue waiting for available resources (server time, cluster node, etc.). Different jobs have different resource requirements, which is why some may run quicker than others. Bowtie runs on our NGS cluster and this can sometimes be very busy. It is important to not stop/restart jobs, or they will start back at the end of the queue. We were very busy earlier this week, but are under less of a usage load right now. I did not find any jobs under this email in the queue, so perhaps your jobs have completed already. If/when you do start new jobs, please be sure to note the yellow banner about NGS tools (Bowtie is one of these) and the maintenance time scheduled for next Monday. Best, Jen Galaxy -- Jennifer Jackson http://galaxyproject.org

ADD COMMENT • link written 6.0 years ago by Jennifer Hillman Jackson ♦ 25k

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