GTF upload error UCSC related to stradedness

Hello,

I’m having issues with uploading a .gtf file to the UCSC browser. I am getting the following error:

“Error GFF/GTF group STRG.155047.1 on chr12+, this line is on chr12-, all group members must be on same seq and strand”

I have previously uploaded .gtf files after converting from mm10 to mm9 using CrossMap.py without any issues. Does anyone have a suggestion for how to get around this error?

This time I first filtered the original .gtf to remove all single-exonic transcripts before converting to mm9 using:

./gffread file.gtf -U -T -o multiexonic.gtf

The resulting file (multiexonic.gtf) has the following structure:

chr1    StringTie   transcript  4807911 4841093 1000    +   .   transcript_id "STRG.187.7"; gene_id "STRG.187"
chr1    StringTie   exon    4807911 4808486 1000    +   .   transcript_id "STRG.187.7"; gene_id "STRG.187";
chr1    StringTie   exon    4828584 4828649 1000    +   .   transcript_id "STRG.187.7"; gene_id "STRG.187";
chr1    StringTie   exon    4830268 4830315 1000    +   .   transcript_id "STRG.187.7"; gene_id "STRG.187";
chr1    StringTie   exon    4832311 4832381 1000    +   .   transcript_id "STRG.187.7"; gene_id "STRG.187";
chr1    StringTie   exon    4837001 4837074 1000    +   .   transcript_id "STRG.187.7"; gene_id "STRG.187";
chr1    StringTie   exon    4840956 4841093 1000    +   .   transcript_id "STRG.187.7"; gene_id "STRG.187";
chr1    StringTie   transcript  4807911 4846739 1000    +   .   transcript_id "STRG.187.4"; gene_id "STRG.187"
chr1    StringTie   exon    4807911 4807982 1000    +   .   transcript_id "STRG.187.4"; gene_id "STRG.187";
chr1    StringTie   exon    4808455 4808486 1000    +   .   transcript_id "STRG.187.4"; gene_id "STRG.187";

Thanks in advance for any and all advice you can provide!