my gtf file cann`t be uploaded to UCSC

[hubenxia123]

Dear Professor,

My name is Benxia Hu,I am a graduate student from Anhui University.Now I am using the software diffsplice to detect alternative splicing. Fortunately, the programme succeed .I get some important result anD I want to visualize the rrsult using the UCSC genome browser.However,I cann`t upload the splice_graph.gtf to UCSC .which gives the follwing Error File 'asm_path.gtf' - Unrecognized format line 3 of custom track: 1 ASM exon 92091 92240 . - . gene_id "1.1"; transcript_id "1.1.p1"; (note: chrom names are case sensitive).\

I first used the RNA-seq data to map the human genome with Ensembl annotation GTF, not UCSC GTF file.

Then I got a aligned.bam file and used it to detect alternative splicing with the software diffsplicing.which output 'asm_path.gtf' .

could you help me ?

Thank you for your attention.

Best wish!

Benxia Hu.

[Brian Lee]

Dear Benxia,

Thank you for using the UCSC Genome Browser and your question about visualizing your custom track in the browser in GTF format.

Looking at your specific example, you are incorrectly referencing the chromosomes in your custom track to be viewed in the UCSC Genome Browser. Please note that you have numbers, 1 for chromosome 1, instead of the proper chromosome names like chr1, necessary to be viewed in the UCSC Genome Browser.

When you encounter an error loading a GFF or GTF track, also check that the data lines contain tabs rather than spaces separating the fields. You can have a line that looks correct, however, if it is not tab-separated you will get an error. You can read more about the format here: http://genome.ucsc.edu/FAQ/FAQformat.html#format3 In the previous FAQ link there is an example you can cut and paste into the browser, and you might experience an error as some paste operations will replace tabs with spaces. In comparison, also provided is a link with tab-separated text that can be directly loaded in the browser to help emphasize this point: http://genome.ucsc.edu/goldenPath/help/regulatory.txt Also, it may be helpful to point out that the GTF portion of the custom track is separated by spaces:http://genome.ucsc.edu/FAQ/FAQformat.html#format4

Here is an example that you can add to the browser based on what you have provided, followed by an explanation where the tabs are spelled out as "-tab-" and the spaces as "-space-": http://hgwdev.cse.ucsc.edu/~brianlee/customTracks/chr1vs1

chr1      ASM         exon       92091        92240      .       -        .         gene_id "1.1"; transcript_id "1.1.p1";

chr1-tab-ASM-tab-exon-tab-92091-tab-92240-tab-.-tab---tab-.-tab-gene_id "1.1";-space-transcript_id "1.1.p1";

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply toge...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee

UCSC Genome Bioinformatics Group

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