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Question: Problem With Bowtie
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gravatar for Law, Michael J.
5.3 years ago by
Law, Michael J. • 20
United States
Law, Michael J. • 20 wrote:
Hello, I am completely new to using galaxy. I have a quick question. I have uploaded my fastq files generated from my experiment for alignments using bowtie. I try to set up the alignment, only to receive the error message that I don't have any sequences with ASCII encoded quality scores. However, when I contact my sequencing facility, they say that the scores are present in the files and that it may be an issue with galaxy. Any help you can provide would be appreciated! Thanks, Mike Michael Law lawmj@rowan.edu<mailto:lawmj@rowan.edu>
alignment bowtie • 1.2k views
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modified 5.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.3 years ago by Law, Michael J. • 20
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gravatar for Ido M. Tamir
5.3 years ago by
Ido M. Tamir • 280
Austria
Ido M. Tamir • 280 wrote:
You should add 10 lines from one of your files. Then its easier to understand the problem. best, ido
ADD COMMENT • link written 5.3 years ago by Ido M. Tamir • 280
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gravatar for Ido M. Tamir
5.3 years ago by
Ido M. Tamir • 280
Austria
Ido M. Tamir • 280 wrote:
the file looks good to me (illumina 1.8 because of the ?). I might have misunderstood the error message. If it comes from galaxy when you try to use this file, then you have not specified the correct file format to galaxy. You have to change its type to fastqsanger by clicking on the pencil. HTH, ido
ADD COMMENT • link written 5.3 years ago by Ido M. Tamir • 280
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gravatar for Jennifer Hillman Jackson
5.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hi MIchael, Glad Ido (thanks!) was able to help - the advise was totally correct, your data does appear to be in .fastqsanger format already and can just be assigned to be recognized by tools. When unsure going forward, run FastQC. If you need more help about working with FASTQ data in Galaxy, see this wiki section and the next for some orientation: http://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset Best, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org
ADD COMMENT • link written 5.3 years ago by Jennifer Hillman Jackson ♦ 25k
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