Read Simulator

Question: Read Simulator

4.8 years ago by

garzetti • 100

Germany

garzetti • 100 wrote:

Dear all, I would like to perforn my SNP calling pipeline (for MySeq Illumina reads) to previously sequenced and assembled genomes. Is there any read simulator in the Main Galaxy? I am looking for something like the wgsim algorithm in SAMtools... Thanks! Debora

samtools bam • 1.0k views

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modified 4.8 years ago by Xianrong Wong • 90 • written 4.8 years ago by garzetti • 100

4.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Debora, There isn't a tool to do this on the public Main Galaxy server at http://usegalaxy.org. But I did just create a ticket to have a wrapped tool in the Tool Shed added to Main for this function. You can "up- vote" to help it become prioritized, and also comment if you have a preference between the choices listed in the description or want to suggest an alternate: https://trello.com/c/z0MLCQHU https://wiki.galaxyproject.org/Issues The Tool Shed's repository "wgsim" could likely be run in a local Galaxy with modest resources without too much trouble. If you want to try, this is how to get started. The repository "grinder" I believe is more compute intensive, but you could test this. Moving to a cloud would work for both. http://getgalaxy.org http://usegalaxy.org/toolshed http://usegalaxy.org/cloud And, one final option is to locate a public Galaxy server that hosts a tool for this function. I don't know of one off hand, but the list of servers is here: https://wiki.galaxyproject.org/PublicGalaxyServers Thanks! Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD COMMENT • link written 4.8 years ago by Jennifer Hillman Jackson ♦ 25k

4.8 years ago by

Xianrong Wong • 90

Xianrong Wong • 90 wrote:

Hi, I've been trying to use the extra DNA tool but I keep getting an error: Traceback (most recent call last): File "/galaxy/main/server/tools/extract/extract_genomic_dna.py", line 300, in if __name__ == "__main__": __main__() File "/galaxy/main/server/tools/extract/extract_genomic_dna.py", line 113, in __main__ I tried it on a dataset which worked 2 days ago but it is failing now too. Jose

ADD COMMENT • link written 4.8 years ago by Xianrong Wong • 90

Hello Jose, We are investigating other similar related problems. Would you please submit the problem as a bug report if you have not already done so and we will follow up with you there. Also, please try to ask questions by starting a new thread (brand new message, new subject line). Do not use "reply" to existing Q & A thread on the mailing list. This helps us with tracking. Best, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org

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