Can you please help me to figure out why the “GFF3_file.expr” was not generated without getting any error message?
I had someone made me a GFF3 file from the KnowGene table; the first lines look like this:
##gff-version 3
gi|89161185|ref|NC_000001.9|NC_000001 UCSC gene 1115 4121 0 + 0 ID=uc001aaa.2gene
gi|89161185|ref|NC_000001.9|NC_000001 UCSC mRNA 1115 4121 0 + 0 ID=uc001aaa.2mRNA;Parent=uc001aaa.2gene
gi|89161185|ref|NC_000001.9|NC_000001 UCSC exon 1115 2090 0 + 0 ID=uc001aaa.2exon1;Parent=uc001aaa.2mRNA
gi|89161185|ref|NC_000001.9|NC_000001 UCSC exon 2475 2584 0 + 0 ID=uc001aaa.2exon2;Parent=uc001aaa.2mRNA
gi|89161185|ref|NC_000001.9|NC_000001 UCSC exon 3083 4121 0 + 0 ID=uc001aaa.2exon3;Parent=uc001aaa.2mRNA
gi|89161185|ref|NC_000001.9|NC_000001 UCSC gene 1115 4272 0 + 0 ID=uc009vip.1gene
gi|89161185|ref|NC_000001.9|NC_000001 UCSC mRNA 1115 4272 0 + 0 ID=uc009vip.1mRNA;Parent=uc009vip.1gene
gi|89161185|ref|NC_000001.9|NC_000001 UCSC exon 1115 2090 0 + 0 ID=uc009vip.1exon1;Parent=uc009vip.1mRNA
gi|89161185|ref|NC_000001.9|NC_000001 UCSC exon 2475 4272 0 + 0 ID=uc009vip.1exon2;Parent=uc009vip.1mRNA
gi|89161185|ref|NC_000001.9|NC_000001 UCSC gene 4268 14764 0 - 0 ID=uc001aab.2gene
gi|89161185|ref|NC_000001.9|NC_000001 UCSC mRNA 4268 14764 0 - 0 ID=uc001aab.2mRNA;Parent=uc001aab.2gene
gi|89161185|ref|NC_000001.9|NC_000001 UCSC exon 4268 4692 0 - 0 ID=uc001aab.2exon1;Parent=uc001aab.2mRNA
gi|89161185|ref|NC_000001.9|NC_000001 UCSC exon 4832 4901 0 - 0 ID=uc001aab.2exon2;Parent=uc001aab.2mRNA
I ran TopHat with the following command:
tophat -r 200 /myDir/bowtie-0.9.9.3/indexes/h_sapiens_asm s_7_1.fastq s_7_2.fastq -G GFF3_knownGene
I had someone made me a GFF3 file from the KnowGene table; the first lines look like this:
##gff-version 3
gi|89161185|ref|NC_000001.9|NC_000001 UCSC gene 1115 4121 0 + 0 ID=uc001aaa.2gene
gi|89161185|ref|NC_000001.9|NC_000001 UCSC mRNA 1115 4121 0 + 0 ID=uc001aaa.2mRNA;Parent=uc001aaa.2gene
gi|89161185|ref|NC_000001.9|NC_000001 UCSC exon 1115 2090 0 + 0 ID=uc001aaa.2exon1;Parent=uc001aaa.2mRNA
gi|89161185|ref|NC_000001.9|NC_000001 UCSC exon 2475 2584 0 + 0 ID=uc001aaa.2exon2;Parent=uc001aaa.2mRNA
gi|89161185|ref|NC_000001.9|NC_000001 UCSC exon 3083 4121 0 + 0 ID=uc001aaa.2exon3;Parent=uc001aaa.2mRNA
gi|89161185|ref|NC_000001.9|NC_000001 UCSC gene 1115 4272 0 + 0 ID=uc009vip.1gene
gi|89161185|ref|NC_000001.9|NC_000001 UCSC mRNA 1115 4272 0 + 0 ID=uc009vip.1mRNA;Parent=uc009vip.1gene
gi|89161185|ref|NC_000001.9|NC_000001 UCSC exon 1115 2090 0 + 0 ID=uc009vip.1exon1;Parent=uc009vip.1mRNA
gi|89161185|ref|NC_000001.9|NC_000001 UCSC exon 2475 4272 0 + 0 ID=uc009vip.1exon2;Parent=uc009vip.1mRNA
gi|89161185|ref|NC_000001.9|NC_000001 UCSC gene 4268 14764 0 - 0 ID=uc001aab.2gene
gi|89161185|ref|NC_000001.9|NC_000001 UCSC mRNA 4268 14764 0 - 0 ID=uc001aab.2mRNA;Parent=uc001aab.2gene
gi|89161185|ref|NC_000001.9|NC_000001 UCSC exon 4268 4692 0 - 0 ID=uc001aab.2exon1;Parent=uc001aab.2mRNA
gi|89161185|ref|NC_000001.9|NC_000001 UCSC exon 4832 4901 0 - 0 ID=uc001aab.2exon2;Parent=uc001aab.2mRNA
I ran TopHat with the following command:
tophat -r 200 /myDir/bowtie-0.9.9.3/indexes/h_sapiens_asm s_7_1.fastq s_7_2.fastq -G GFF3_knownGene
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