hello
I am currently trying to do RNA-seq using public data in brassica juncea.
To use htseq-count for making count table, I have to convert gff file which downloaded in brassica database to gtf file.
So I used gffread for converting gff file with below command
gffread Bju.genome.gff -T -o Bju.genome.gtf
But when I type above command, I got a lot of error message like below
Error: discarding overlapping duplicate mRNA feature (24650-31472) with ID=BjuO004617
Error: discarding overlapping duplicate mRNA feature (39979-40535) with ID=BjuO004618
Error: discarding overlapping duplicate mRNA feature (30824-34680) with ID=BjuO001651
Error: discarding overlapping duplicate mRNA feature (56651-57957) with ID=BjuO001652
Error: discarding overlapping duplicate mRNA feature (78160-80198) with ID=BjuO001654
Error: discarding overlapping duplicate mRNA feature (74204-77329) with ID=BjuO001653
Error: discarding overlapping duplicate mRNA feature (4453-4737) with ID=BjuO006559
Error: discarding overlapping duplicate mRNA feature (10094-10618) with ID=BjuO009958
Error: discarding overlapping duplicate mRNA feature (15520-17470) with ID=BjuO010812
Error: discarding overlapping duplicate mRNA feature (22118-22816) with ID=BjuO010813
Error: discarding overlapping duplicate mRNA feature (5722-6432) with ID=BjuO010811
Error: discarding overlapping duplicate mRNA feature (3944-4429) with ID=BjuO007439
Error: discarding overlapping duplicate mRNA feature (790-2307) with ID=BjuO007438
Error: discarding overlapping duplicate mRNA feature (6457-6978) with ID=BjuO005411
To check if the file was created properly, I checked file size.
And it looks like ok.
40M Bju.genome.gff
56M Bju.genome.gtf
and I also used ‘head’ command, and there seems to be no problem
A01 GeneWise gene 3352 5985 1195.88 + . ID=BjuA000594;
A01 GeneWise mRNA 3352 5985 1195.88 + . ID=BjuA000594;Parent=BjuA000594;
A01 GeneWise CDS 3352 3675 1195.88 + 0 ID=BjuA000594.cds;Parent=BjuA000594;
A01 GeneWise CDS 4225 4447 1195.88 + 0 ID=BjuA000594.cds;Parent=BjuA000594;
A01 GeneWise CDS 4579 4949 1195.88 + 2 ID=BjuA000594.cds;Parent=BjuA000594;
A01 GeneWise CDS 5091 5326 1195.88 + 0 ID=BjuA000594.cds;Parent=BjuA000594;
A01 GeneWise CDS 5421 5691 1195.88 + 1 ID=BjuA000594.cds;Parent=BjuA000594;
A01 GeneWise CDS 5785 5985 1195.88 + 0 ID=BjuA000594.cds;Parent=BjuA000594;
A01 GeneWise gene 8012 14242 1731.69 + . ID=BjuA002557;
A01 GeneWise mRNA 8012 14242 1731.69 + . ID=BjuA002557;Parent=BjuA002557;
So, I wonder why the error message appeared and whether it is okay to use the created file.
I would be really grateful if someone reply.
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