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Question: Split barcodes tool output
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gravatar for leeman.rebecca
4.4 years ago by
leeman.rebecca • 0
United States
leeman.rebecca • 0 wrote:

Hello,

    It seems that the output for the split barcodes tool is text files (txt) rather than fastq. Is there a way to turn these into fastq files so that they will be recognized as such by analysis software? Thank you!
galaxy • 1.1k views
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modified 4.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.4 years ago by leeman.rebecca • 0
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gravatar for Jennifer Hillman Jackson
4.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

An easy way to get these output files back into you Galaxy history is by right-clicking to copy the link to the files from the table (paste these into a text file, saves time if there are multiple), then open the "Get Data -> Upload File" tool and paste in those URLs. Submit.

The data will load, reassign the datatype as ".fastqsanger", and you'll be ready to continue. I haven't done this in a while, so let us know if you have any problems.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 4.4 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen, Thanks so much for your help. I am about to try this but in the meantime wanted to ask about something else: The software that I'm using for my analysis (proprietary software from Agilent for the specific library prep kit I used) only recognizes FASTQ files (not "fastqsanger" for example). Is there any way of turning these fastqsanger files into just fastq so they'll be recognized? Thank you! Rebecca

ADD REPLY • link written 4.4 years ago by leeman.rebecca • 0
1

Hi Rebecca,

fastqsanger is a fastq file just with a "different" encoding. Please read the following about the different fastq encodings.

http://en.wikipedia.org/wiki/FASTQ_format#Encoding

I'm pretty sure your expensive program can process these files. If not you can use the "FASTQ Groomer convert between various FASTQ quality formats" tool to convert it to any other fastq format.

Cheers,

Bjoern

ADD REPLY • link written 4.4 years ago by Bjoern Gruening ♦ 5.1k
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