Bowtie don't load paired end data

Question: Bowtie don't load paired end data

4.3 years ago by

Italy

Hi, I'm new in the NGS technology. I have a problem with Bowtie paired end loading data. A few weeks ago I use galaxy to generating data from my Illumina Fastq: I convert format to fastqsanger using the convert format tab on ''edit attributes''. Now it's impossible! I convert format with fastq groomer but, when I try to starting alignment with bowtie for Illumina, I choose paired end but the software don't show me the possibility to load two fastqsanger files. I don't understand why, cause I did it some a few weeks ago...

I try to start with only one (forward file or reverse) and obviously in the bam files I see nothing. I hope to have explained my problem in a good manner (I'm not a bioinformaticist).

Thanks

bowtie galaxy • 1.5k views

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modified 4.3 years ago • written 4.3 years ago by stefano.diani • 0

4.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Both 'Bowtie for Illumina" and "Bowtie2" on the public Main Galaxy instance (http://usegalaxy.org) have an option on the form named "Is this library mate-paired?:". Make certain this is set to paired.

If you are using this on a local/cloud, the wrappers from the devteam and iuc will most closely match those on the public Main instance. Should you be using the tool at another public Galaxy site, tools can vary - if you do not find this option (would be odd, but possible), then contacting the host of the instance is the way forward.

Hopefully the first suggestion clears things up! Jen, Galaxy team

ADD COMMENT • link written 4.3 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen,

thanks for your reply. As i wrote in my message I did the same process a few days ago and I see the form for mate paired end, but after I can`t load two different fastqsanger files (R1 and R2) but the software show one only possibility to loading. When I did it days ago, after I choose paired end, the software shows another drop down box to load both pair files.

Thaks

Stefano

ADD REPLY • link written 4.3 years ago by stefano.diani • 0

Very odd. Where are you running the tool? Jen

ADD REPLY • link written 4.3 years ago by Jennifer Hillman Jackson ♦ 25k

4.3 years ago by

stefano.diani • 0

Italy

stefano.diani • 0 wrote:

Hi Jen, sorry I don't understand ''where''?

ADD COMMENT • link written 4.3 years ago by stefano.diani • 0

Hi Stefano -- I think Jen was asking which server you're using. Are you using usegalaxy.org or a different Galaxy server?

ADD REPLY • link written 4.3 years ago by Dannon Baker ♦ 3.7k

4.3 years ago by

stefano.diani • 0

Italy

stefano.diani • 0 wrote:

Hi Dannon, I'm using usegalaxy.org

ADD COMMENT • link written 4.3 years ago by stefano.diani • 0

Hi Stefano, I just re-tested both "Map with Bowtie for Illumina" and "Bowtie2" on the public Main Galaxy instance (http://usegalaxy.org). When the option for paired is selected, the form resets to permit two .fastq input files. The form refresh occurs quickly (about a second). Would you please try this again? Thanks, Jen, Galaxy team

ADD REPLY • link written 4.3 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen, I don't know why but with another browser (Chrome) it's running! With explorer bowtie don't run again.

ADD REPLY • link written 4.3 years ago by stefano.diani • 0

Which version of internet explorer is this?

ADD REPLY • link written 4.3 years ago by Dannon Baker ♦ 3.7k

Hi Dannon, it's version 11. Now I see that I set both the paired end files but bowtie don't start, is waiting to run... what it happens?

ADD REPLY • link written 4.3 years ago by stefano.diani • 0

Thanks for the info, I'm surprised IE11 is having issues with the tool form but I'll take a look.

Regarding the job, depending on the current load on our systems, it might stay in the 'waiting to run' state for a (usually brief) period of time until resources are available to run it. Things are probably fine, just wait on it to complete at this point.

ADD REPLY • link written 4.3 years ago by Dannon Baker ♦ 3.7k

When I wrote last message the system goes to the end. Thanks

ADD REPLY • link written 4.3 years ago by stefano.diani • 0

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