Alex, Thanks that worked. I was thrown off by the word concatenate, which I mistakenly thought would join reads together (reads remain separate), and by the absence of the word merge, which is used when referring to combining two BAM datasets together in Galaxy. It seems to me that the tool to combine BAM datasets, "Merge Bam Files", and the tool to combine FASTQ datasets, "Concatenate datasets" work the same but "Concatenate datasets" works on any type of dataset. Edward On Dec 27, 2011, at 11:02 AM, Bossers, Alex wrote:

Edward, If you just want to conacatenate the fastq files (I assume that is what you mean) you can do that using the text manipulation tools: concatenate datasets tail-to-head. Good luck. Alex

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Van: galaxy-user-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] namens Edward Turk [edwardturk@mac.com] Verzonden: zaterdag 24 december 2011 3:30 Aan: galaxy-user@lists.bx.psu.edu Onderwerp: [galaxy-user] Merge FASTQ Databases

Hi Galaxy Users,

Can FASTQ Databases be merged using Galaxy?

Thanks, Edward ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

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Ateeq,

The preferred method for uploading large files (that aren't already hosted somewhere) is FTP. See the instructions here: http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP

We don't generally provide specific analysis pipelines, rather the tools for composing them, though you're welcome to look through the shared workflows, histories, and pages (See "Shared Data" in Galaxy) for examples and perhaps someone else will chime in with their experiences analyzing bacterial transcriptomes.

Lastly, try not to piggyback on unrelated threads (as in your other email). It makes tracking email replies more difficult.

-Dannon

On Jan 9, 2012, at 10:30 AM, Ateequr Rehman wrote:

Dear galaxy Users

I am very very new to galaxy, will be highly obliged if some one could help me to find the way to analyse bacterial tramnscriptome. in the first step itself , i am having trouble to upload files...

Does any one knows how to generate URL to upload data, my fastq files are about 3 gb each,

Is there any specific pipeline to analyse bacterial transcriptome

Thanking all of you

Ateeq ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

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