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Question: FASTQ files in history but cannot add to tasks like FASTQ trimmer or TopHat2
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gravatar for james.lloyd
4.4 years ago by
james.lloyd • 0
United States
james.lloyd • 0 wrote:

I am a new user and uploaded to large FASTQ files which galaxy recognises as FASTQ files. However when I go to the FASTQ Trimmer or TopHat2, those files are not available from the drop down menu and I don't know why. I have added a database to the files (TAIR10) but still I cannot select them. I am sure it is something simple I am missing but as I am new help would be appreciated. 

 

Thanks. 
fastq tophat galaxy rna-seq • 1.8k views
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modified 4.4 years ago • written 4.4 years ago by james.lloyd • 0
0
gravatar for Bjoern Gruening
4.4 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi,

uploaded fastq files will be recognised as 'fastq' format. TopHat and related tools only takes inputs in 'fastqsanger' format. You can easily change the filetype of your dataset.

Read more about managing datsets in Galaxy here:

https://wiki.galaxyproject.org/Learn/ManagingDatasets?action=show&redirect=Learn%2FManaging+Datasets

And about the fastq format here:

http://en.wikipedia.org/wiki/FASTQ_format

Ciao,

Bjoern
ADD COMMENT • link written 4.4 years ago by Bjoern Gruening ♦ 5.1k
0
gravatar for james.lloyd
4.4 years ago by
james.lloyd • 0
United States
james.lloyd • 0 wrote:

I have changed the file types to fastqcsanger and they are recognised now so I can trim the sequence length. Many thanks for your help and I will certainly read more about galaxy. 

 

Many thanks!!! 

James
ADD COMMENT • link written 4.4 years ago by james.lloyd • 0
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