Cannot select fastq data in Galaxy Trimmomatic

Question: Cannot select fastq data in Galaxy Trimmomatic

20 months ago by

g.gouws • 20 wrote:

Hi Galaxy-verse

I am trying to open my uploaded paired-end MiSeq reads in Trimmomatic from within Galaxy. The picklist for the field for the second set of reads (R2) lets me choose the relevant data set from my uploaded data, but the field for the first (R1) is non-operable. It doesn't let me enter any information and the picklist dropdown does not seem to work either. It is just populated with a message about there not being any fastq data available. I initially thought it might be a browser issue, but no luck. Nothing. Seems to be blocked, and the problem persists across Chrome, IE and Firefox.

Appreciate any help.

galaxy • 843 views

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modified 18 months ago by thomas.enriquez.tours • 10 • written 20 months ago by g.gouws • 20

How-to help for fastqsanger dataset input is here, for any others reading: https://galaxyproject.org/support/#getting-inputs-right-

ADD REPLY • link written 18 months ago by Jennifer Hillman Jackson ♦ 25k

20 months ago by

Mo Heydarian ♦ 830

United States

Mo Heydarian ♦ 830 wrote:

Hello, Can you check the format/datatype of your data? Are both the R1 and R2 samples in fastqsanger format? If not, you can change the format by clicking the pencil icon (associated with each dataset) assigning the datatype under the "Datatype" tab.

Hope this helps.

Thanks for using Galaxy!

Cheers, Mo Heydarian

ADD COMMENT • link written 20 months ago by Mo Heydarian ♦ 830

18 months ago by

g.gouws • 20

g.gouws • 20 wrote:

Hey there,

I was reluctant to change the data format, because to my mind it was reading the data just fine in the second field. Didn't think there was anything wrong with the data. I eventually relented and used FASTQCGroomer to check and the edit attribute in FASTQC to change the format to fastqsanger. Worked fine in all downstream apps after that...

Good luck!

ADD COMMENT • link written 18 months ago by g.gouws • 20

18 months ago by

thomas.enriquez.tours • 10

thomas.enriquez.tours • 10 wrote:

Hello, I just changed the format using Fastq Groomer and now I can select my data with Trimmomatic! Thank's a lot for your help. Best, Thomas

ADD COMMENT • link written 18 months ago by thomas.enriquez.tours • 10

20 months ago by

g.gouws • 20

g.gouws • 20 wrote:

Hi Mo,

Thanks for the quick reply. I don't think it is a data format issue. The R2 field can recognise and capture the relevant R2 data file (and even the R1 file), but not the R1 field (which seems inactive). I tried converting the format as suggested, but the same thing happens. The R2 field is operable, but not the first.

I still suspect some kind of browser issue, so I'll carry on fidgeting.

ADD COMMENT • link written 20 months ago by g.gouws • 20

18 months ago by

thomas.enriquez.tours • 10

thomas.enriquez.tours • 10 wrote:

Hello, I have exactly the same problem with Trimmomatic, Tophat2, Bowtie... The R1 field don't allow me to select any FastQ file, but the R2 field does (R1 and R2 FastQ) g.gouws: Did you resolve this problem? Best, Thomas

ADD COMMENT • link written 18 months ago by thomas.enriquez.tours • 10

Sorry! Tried to comment directly so that you would be alerted to the response, but it just posted it as another comment in the thread...

ADD REPLY • link written 18 months ago by g.gouws • 20

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