Error Uploading file as custom track

[Cydric G.]

Dear Genome Browser Team,

I would like to upload this file (see appendix) as a custom track, but i get an error saying: 

Error File 'UROD_Mb_geneid.gff' - invalid unsigned integer: "geneid_v1.2"

How can i fix this?

Thanks in advance,

Cydric G.

[Cath Tyner]

Hello Cydric,

Thank you for contacting the UCSC Genome Browser support team. I was able to replicate the same error that you are seeing. Since your file appears to match gff2 standards, I thought that there might be a problem with hidden characters. 

I performed the following steps to fix the file:

First, I cut out all 9 columns:

cat UROD_Mb_geneid.gff | cut -f1,2,3,4,5,6,7,8,9 -d$'\t' > new.gff

I then replaced spaces with tabs:

awk -v OFS="\t" '$1=$1' new.gff

I was able to successfully upload "new.gff" as a custom track into hg38, as seen in this hg38 session. 

I have also attached 'new.gff' with this response. 

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. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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