The fimo.gff file was not accepted by the UCSC Genome Table Browser

[Qian Qiu]

When I used the GFF3 file fimo.gff as input for uploading to the UCSC Genome Table Browser, the following error occurred:  

Error

invalid unsigned integer: "fimo"

my gff file: 

##gff-version 3 NC_000020.11 fimo nucleotide_motif 5909790 5909797 44 - . Name=MA0867.3_NC_000020.11-;Alias=SOX4;ID=MA0867.3-SOX4-1-NC_000020.11;pvalue=3.96e-05;qvalue=0.118;sequence=AACAAAGA; NC_000020.11 fimo nucleotide_motif 5910115 5910122 42.4 - . Name=MA0867.3_NC_000020.11-;Alias=SOX4;ID=MA0867.3-SOX4-2-NC_000020.11;pvalue=5.75e-05;qvalue=0.118;sequence=AACAATGG;

my uploaded sequence like:

>NC_000020.11:5909510-5911609 Homo sapiens chromosome 20, GRCh38.p14 Primary Assembly TATTCTTTTTTCAATTTTAAAAGTATTTCAGATTTCAGAAAAATGCAAAAATAGTAAAAAAAATTCCCTTATACCTTTCTCCTCAATTCCCTGAATGTTA ACATTTTGCCATACTTACCTTAGCATTCTCTTTTTCTCTATCTTTATATTTTTTTCTAAAAATGTGAAAGGAAGTTGTACATATGATACCCTTTTACACC TAGTCACTTCAAGATGTGTTTCCTAAAAACAGGGACATTTTCTTACATAATCACAGTACAATTTTCTTTCTCTCTCTCTTTCTTTGTTTTTCTTTTCTTT

What is the problem with this?

[tlawb...@gmail.com]

Hi erzach,

It appears your GFF file has been processed or corrupted in some way.

Maybe someone cut-and-pasted it into a different file?

MEME Suite GFF files are Plain Text files.  There is supposed to be

a newline after the "##gff-version 3" but that seems to have disappeared

so the first and second lines are run together.  That would explain the error

given by the UCSC Genome Table Browser.

If you input the GFF file output by FIMO directly to the browser, without doing

anything to it, it should be accepted by the Genome Table Browser.

T.