Extract Genomic DNA Invalid Lines Error

usegalaxy.org support
, , ,
8

Thank you @jennaj for the suggestions. I was able to resolve the issue by the following:

  1. Split my large file containing the ORFs of interest (~47 000 sequences) into separate files each containing 500 sequences each

  2. Used one of the files produced from the above step to find putative primers and generate a bed file with the coordinates (Used Primer3).

  3. Created a custom build on galaxy using the file (same one as selected for Step 2) that I used to find the primers. This same file was also used as the reference genome for the Extract Genomic DNA search.

  4. Assigned the bed file and the reference genome to the custom build.

  5. Success running Extract Genomic DNA.

I actually didn’t need to normalize the data following procedure, but that may have been happy coincidence.

Thanks again for the suggestions!

Andrea

1 Like