Using Files Produced By "Barcode Splitter"

Question: Using Files Produced By "Barcode Splitter"

7.4 years ago by

I used the "Barcode Splitter" tool to split multiplexed RNA-Seq libraries into separate files. I would now like to map the reads from each of these fastq files to a reference genome. However, the fastq files generated by Barcode Splitter don't appear in the "Fastq File" pull-down menus within the the BWA or Bowtie launch pages. I'm probably missing something obvious, but what is the trick for making these files available for the mapping tools? Do I need to import them into my history somehow? Thanks! Jeremy

bwa alignment bowtie • 1.6k views

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modified 7.4 years ago by Jim Johnson • 40 • written 7.4 years ago by Jeremy Coate • 70

7.4 years ago by

David K Crossman • 130

United States

David K Crossman • 130 wrote:

Jeremy, The files need to be groomed using the FastQ Groomer so that they will end up in the fastqsanger state. Then your files will show up in the pull-down menus. David To: galaxy-user@lists.bx.psu.edu Subject: [galaxy-user] using files produced by "Barcode Splitter" I used the "Barcode Splitter" tool to split multiplexed RNA-Seq libraries into separate files. I would now like to map the reads from each of these fastq files to a reference genome. However, the fastq files generated by Barcode Splitter don't appear in the "Fastq File" pull-down menus within the the BWA or Bowtie launch pages. I'm probably missing something obvious, but what is the trick for making these files available for the mapping tools? Do I need to import them into my history somehow? Thanks! Jeremy

ADD COMMENT • link written 7.4 years ago by David K Crossman • 130

Thanks David, I had considered this possibility but, curiously, the files don't show up in the FastQ Groomer pull-down menu either. The original (multiplexed) data file that I split using the Barcode Splitter is there (and, incidentally, I ran FastQ Groomer on that before doing the barcode split), but none of the 3 files resulting from the splitter show up. Any other thoughts? It seems like the new files just aren't landing in my history, though I can look at them by clicking their links from the Barcode Splitter output. Jeremy

ADD REPLY • link written 7.4 years ago by Jeremy Coate • 70

7.4 years ago by

Jim Johnson • 40

Jim Johnson • 40 wrote:

I've had users make a similar request for the split files to appear in their history. I made my own wrapper to enable this behavior. It presents a list of barcodes from the barcode file input. Any barcodes the user selects will have the resulting files copied to the users history as new datasets. I uploaded my barcode splitter tool configs to the toolshed: http://toolshed.g2.bx.psu.edu/ as repository: barcode_splitter JJ Date: Mon, 18 Jul 2011 13:33:58 -0700 From: Jeremy Coate <jec73@cornell.edu> To: David K Crossman <dkcrossm@uab.edu> Cc: "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu> Subject: Re: [galaxy-user] using files produced by "Barcode Splitter" Message- ID: <caa2bwd5ueraqeoueq97tfnhkwvhziq89whvr-oy04ov- k4ju6q@mail.gmail.com=""> Content-Type: text/plain; charset="iso-8859-1" Thanks David, I had considered this possibility but, curiously, the files don't show up in the FastQ Groomer pull-down menu either. The original (multiplexed) data file that I

ADD COMMENT • link written 7.4 years ago by Jim Johnson • 40

7.4 years ago by

Jim Johnson • 40

Jim Johnson • 40 wrote:

Jeremy, Usually, the users saved the files to their local machine by clicking on the links, and then uploaded them again to the galaxy server. It can be possible to copy the link location, and paste it into the upload tools URL textarea. Ideally, it would be nice for the tool developer to be able to include a link in the html that would "promote" the file to a dataset in the current history. JJ

ADD COMMENT • link written 7.4 years ago by Jim Johnson • 40

Ah ha - thanks. I was trying to click the link, but it kept crashing, presumably because the files are too big. The URL method seems to work, though. I agree that it would be nice if there was a way to bump the files directly into your history without the download/upload steps. Thanks again for the help. Jeremy

ADD REPLY • link written 7.4 years ago by Jeremy Coate • 70

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