Hi All
I'm trying to use tophat with the --GFF argument so as to get RPKM data for some yeast experiments. My question is that the .junc file produced by tophat seems not to be consistent with the exon data supplied in the GFF file. For example, when the GFF specifies
Scchr01 SGD gene 87287 87753 . + . ID=YAL030W
Scchr01 SGD mRNA 87287 87753 . + . ID=YAL030WmRNA;Parent=YAL030W
Scchr01 SGD exon 87287 87388 . + 0 ID=YAL030Wexon1;Parent=YAL030WmRNA
Scchr01 SGD exon 87502 87753 . + 0 ID=YAL030Wexon2;Parent=YAL030WmRNA
the .junc file specifies
Scchr01 87387 87501 +
The position 87387 appears incorrect if it is suppose to be indicating the first base of the intron (as 87501 appears to indicate the last position of the intron) or even the last base of the exon. Am I misinterpreting this or is there a problem here?
Thanks for your help
I'm trying to use tophat with the --GFF argument so as to get RPKM data for some yeast experiments. My question is that the .junc file produced by tophat seems not to be consistent with the exon data supplied in the GFF file. For example, when the GFF specifies
Scchr01 SGD gene 87287 87753 . + . ID=YAL030W
Scchr01 SGD mRNA 87287 87753 . + . ID=YAL030WmRNA;Parent=YAL030W
Scchr01 SGD exon 87287 87388 . + 0 ID=YAL030Wexon1;Parent=YAL030WmRNA
Scchr01 SGD exon 87502 87753 . + 0 ID=YAL030Wexon2;Parent=YAL030WmRNA
the .junc file specifies
Scchr01 87387 87501 +
The position 87387 appears incorrect if it is suppose to be indicating the first base of the intron (as 87501 appears to indicate the last position of the intron) or even the last base of the exon. Am I misinterpreting this or is there a problem here?
Thanks for your help
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