Hi all,
I try to use tophat GFF option, but met some problems. I downloaded the gtf format of Refseq genes from UCSC, and then convert it to gff3 format. But when I feed tophat this file, it returns no junctions were found. I have checked the log file. It has some errors like: "No transcript with id NR_024540".
Here is NR_024540 gene in my gff3 files:
Is something wrong with my gff3 file ? does someone have any ideas ?
Thanks.
I try to use tophat GFF option, but met some problems. I downloaded the gtf format of Refseq genes from UCSC, and then convert it to gff3 format. But when I feed tophat this file, it returns no junctions were found. I have checked the log file. It has some errors like: "No transcript with id NR_024540".
Here is NR_024540 gene in my gff3 files:
Code:
chr1 hg19_refGene gene 14363 29370 . - . ID=NR_024540 chr1 hg19_refGene mRNA 14363 29370 . - . ID=NR_024540_mRNA;Parent=NR_024540 chr1 hg19_refGene exon 14363 14829 . - . ID=NR_024540_exon11;Parent=NR_024540 chr1 hg19_refGene exon 14970 15038 . - . ID=NR_024540_exon10;Parent=NR_024540 chr1 hg19_refGene exon 15796 15947 . - . ID=NR_024540_exon9;Parent=NR_024540 chr1 hg19_refGene exon 16607 16765 . - . ID=NR_024540_exon8;Parent=NR_024540 chr1 hg19_refGene exon 16858 17055 . - . ID=NR_024540_exon7;Parent=NR_024540 chr1 hg19_refGene exon 17233 17368 . - . ID=NR_024540_exon6;Parent=NR_024540 chr1 hg19_refGene exon 17606 17742 . - . ID=NR_024540_exon5;Parent=NR_024540 chr1 hg19_refGene exon 17915 18061 . - . ID=NR_024540_exon4;Parent=NR_024540 chr1 hg19_refGene exon 18268 18366 . - . ID=NR_024540_exon3;Parent=NR_024540 chr1 hg19_refGene exon 24738 24891 . - . ID=NR_024540_exon2;Parent=NR_024540 chr1 hg19_refGene exon 29321 29370 . - . ID=NR_024540_exon1;Parent=NR_024540
Thanks.