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Galaxy cannot recognize the uploaded fastq
I try to use Tophat to do RNA analysis on Galaxy. I uploaded a fastq file. But there is no choices for that dataset. See detailed in screenshots.
I am wonder if there is something wrong with the format of the fastq file.
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I try to use Tophat to do RNA analysis on Galaxy. I uploaded a fastq file. But there is no choices for that dataset. See detailed in screenshots.
I am wonder if there is something wrong with the format of the fastq file. -
You need to say what kind of FASTQ it is, e.g. Sanger or Illumina. Click on the history entry's pencil button to edit this -
it may be tangential, but useful to know that it's not the most standard FASTQ format, it's come from the NCBI Sequence Read Archive which is why it contains more metadata than you might expect (i.e. on the + line prior to the qualities)Comment
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(Leaving aside colour space) the FASTQ files from the NCBI SRA are standard Sanger encoded, but yes, they do have different meta data in the free description line to what you'd see from the original instrument.Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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