uploaded FASTQ not showning in the pulldown menu

Question: uploaded FASTQ not showning in the pulldown menu

4.5 years ago by

Taiwan

mychung • 0 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 • 1.4k views

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modified 4.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.5 years ago by mychung • 0

4.5 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k 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 COMMENT • link written 4.5 years ago by Bjoern Gruening ♦ 5.1k

Hi Jennifer and Bjoern,

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

ADD REPLY • link written 4.5 years ago by mychung • 0

4.5 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 4.5 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jennifer and Bjoern,

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

ADD REPLY • link written 4.5 years ago by mychung • 0

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