Help formatting FASTQ manifest file

Similar to the problems above, I am also having issues importing ion torrent fastq files. Again I have one fastq file per sample which has been demultiplexed.

I have created the se-33-manifest.csv file and have modified in many different ways with no success…

The error keep getting is:

‘se-33-manifest.csv is not a(n) SingleEndFastqManifestPhred33 file’

Any help/advice would be much appreciated??

Hi @PLD,
It sounds like you are running into the same issues as this thread. Please read through that thread to see if a solution already exists. Do you have a header line in your manifest file?

If all else fails, please share:

  1. your manifest file
  2. a list of the files that you are attempting to import.
  3. the first few lines of one of your fastqs, so we can make sure this is not a formatting issue.

Good luck!

Hi Nicholas,
Thanks for the help, I found a way to make it work. Seems the excel sheet was adding something else to the document.



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