Question: uploaded FASTQ not showning in the pulldown menu
0
gravatar for mychung
3.8 years ago by
mychung0
Taiwan
mychung0 wrote:

Hi,

 

I FTPed .fastq.gz files to Galaxy server and uploaded to Galaxy (appear in the history menu). But when analyze data using "Mapping with Bowtie for Illumina", the files are not showning up in the pulldown menu for "FASTQ file". Thank you for help.

 

Maggie

alignment • 1.1k views
ADD COMMENTlink modified 3.8 years ago by Jennifer Hillman Jackson24k • written 3.8 years ago by mychung0
1
gravatar for Bjoern Gruening
3.8 years ago by
Bjoern Gruening4.9k
Germany
Bjoern Gruening4.9k wrote:

Hi Maggie,

uploaded fastq files will be recognised as 'fastq' format. The Bowtie Tool only takes inputs in 'fastqsanger' format. If you are sure you uploaded file is in the 'sanger' encoded fastq format you can easily change the filetype of your dataset to 'fastqsanger'. Otherwise, you can convert your fastq file to the sanger format with the 'fastq groomer'.

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 COMMENTlink written 3.8 years ago by Bjoern Gruening4.9k

Hi Jennifer and Bjoern,

Thank you both for help. It worked after converting by "fastq groomer".

ADD REPLYlink written 3.8 years ago by mychung0
1
gravatar for Jennifer Hillman Jackson
3.8 years ago by
United States
Jennifer Hillman Jackson24k wrote:

Hi Maggie,

Bjoern has all the good info, so I'll just add in that we have some support resources that cover this same basic info. How to investigate what type of quality score format you have in any starting data plus if and how to groom or directly assign datatype here in our wiki: https://wiki.galaxyproject.org/Support#Dataset_special_cases

The link above includes a link to a Vimeo video I made that walks-through the processing step-by-step, if you are new to Galaxy or just want to see how it is done exactly in the web interface. Also here: http://vimeo.com/galaxyproject/fastqprep

Thanks all! Jen, Galaxy team

ADD COMMENTlink written 3.8 years ago by Jennifer Hillman Jackson24k

Hi Jennifer and Bjoern,

Thank you both for help. It worked after converting by "fastq groomer".

ADD REPLYlink written 3.8 years ago by mychung0
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