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  • Trouble formatting GTF file for UCSC genome browser

    Hi all, I need some help with something you probably think is very easy.

    I am trying to upload a custom track of an annotated genome into the UCSC genome browser to analyze some sequencing data I just got. Specifically, I am trying to upload a GTF file. When I do, I get the error:
    " Error File 'FormattingTest.csv' - Unrecognized format line 6 of custom track: chr RefSeq region 1 2821361 . + . gene_id “id0”; transcript_id “id0”; (note: chrom names are case sensitive) "

    I have copied and pasted the line in question directly from the file into the upload box and tested to be sure that the values are separated by tabs not spaces (as this was listed in other forums as one of the most common errors). I have also tried just copying and pasting the examples from the UCSC help pages, and I get the same error. I just can't make it work. Anybody know what might be going wrong?

    Thanks

    David

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