Merge Fastq Databases

Question: Merge Fastq Databases

6.9 years ago by

Edward Turk • 100

Edward Turk • 100 wrote:

Hi Galaxy Users, Can FASTQ Databases be merged using Galaxy? Thanks, Edward

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modified 3.7 years ago by nls5231 • 0 • written 6.9 years ago by Edward Turk • 100

6.9 years ago by

Bossers, Alex • 240

Bossers, Alex • 240 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 ________________________________________ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

ADD COMMENT • link written 6.9 years ago by Bossers, Alex • 240

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

ADD REPLY • link written 6.9 years ago by Edward Turk • 100

6.9 years ago by

Ateequr Rehman • 150

Ateequr Rehman • 150 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

ADD COMMENT • link written 6.9 years ago by Ateequr Rehman • 150

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

ADD REPLY • link written 6.9 years ago by Dannon Baker ♦ 3.7k

3.7 years ago by

nls5231 • 0

United States

nls5231 • 0 wrote:

Give me the way to merge FASTQ files

ADD COMMENT • link modified 3.7 years ago • written 3.7 years ago by nls5231 • 0

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