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Old 11-04-2010, 05:19 PM   #1
dingkai0564
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Location: lasvegas

Join Date: Nov 2010
Posts: 10
Default looking for solution to count the short reads in rice

recently i am analyzing the RNA-seq in rice.However,when i want to use tophat or HTseq to analysis my illumina data, it seems that it need GTF file.However, I only have the GFF3 file.Could anybody told me how to convert the GFF3 file to the GTF file so that i can use the HTseq to count my short reads.

Here is the top lines of my GFF3 files:

##gff-version 3
##genome-build MSU Rice Genome Annotation Project osa1r6
##species Oryza sativa spp japonica cv Nipponbare
##sequence-region Chr1 1 43268879
Chr1 MSU_osa1r6 gene 1903 9817 . + . ID=13101.t00001;Name=TBC%20domain%20containing%20protein%2C%20expressed;Alias=LOC_Os01g01010
Chr1 MSU_osa1r6 mRNA 1903 9817 . + . ID=13101.m00001;Parent=13101.t00001;Alias=LOC_Os01g01010.1
Chr1 MSU_osa1r6 five_prime_UTR 1903 2268 . + . Parent=13101.m00001
Chr1 MSU_osa1r6 five_prime_UTR 2354 2448 . + . Parent=13101.m00001
Chr1 MSU_osa1r6 CDS 2449 2616 . + 0 Parent=13101.m00001
Chr1 MSU_osa1r6 CDS 3357 3455 . + 0 Parent=13101.m00001
Chr1 MSU_osa1r6 CDS 4457 4560 . + 0 Parent=13101.m00001
Chr1 MSU_osa1r6 CDS 6136 6944 . + 2 Parent=13101.m00001
Chr1 MSU_osa1r6 CDS 7028 7150 . + 1 Parent=13101.m00001
Chr1 MSU_osa1r6 CDS 7232 7320 . + 1 Parent=13101.m00001
Chr1 MSU_osa1r6 CDS 7408 7608 . + 0 Parent=13101.m00001
Chr1 MSU_osa1r6 CDS 8210 8617 . + 0 Parent=13101.m00001
Chr1 MSU_osa1r6 CDS 9104 9187 . + 0 Parent=13101.m00001
Chr1 MSU_osa1r6 CDS 9274 9297 . + 0 Parent=13101.m00001
Chr1 MSU_osa1r6 three_prime_UTR 9298 9430 . + . Parent=13101.m00001
Chr1 MSU_osa1r6 three_prime_UTR 9504 9817 . + . Parent=13101.m00001
###
Chr1 MSU_osa1r6 mRNA 1984 9562 . + . ID=13101.m00002;Parent=13101.t00001;Alias=LOC_Os01g01010.2
Chr1 MSU_osa1r6 five_prime_UTR 1984 2255 . + . Parent=13101.m00002
Chr1 MSU_osa1r6 five_prime_UTR 2354 2448 . + . Parent=13101.m00002
Chr1 MSU_osa1r6 CDS 2449 2616 . + 0 Parent=13101.m00002
Chr1 MSU_osa1r6 CDS 3357 3455 . + 0 Parent=13101.m00002
Chr1 MSU_osa1r6 CDS 4457 4560 . + 0 Parent=13101.m00002
Chr1 MSU_osa1r6 CDS 6136 6944 . + 2 Parent=13101.m00002
Chr1 MSU_osa1r6 CDS 7028 7150 . + 1 Parent=13101.m00002
Chr1 MSU_osa1r6 CDS 7232 7320 . + 1 Parent=13101.m00002
Chr1 MSU_osa1r6 CDS 7408 7608 . + 0 Parent=13101.m00002
Chr1 MSU_osa1r6 CDS 8210 8311 . + 0 Parent=13101.m00002
Chr1 MSU_osa1r6 CDS 9104 9187 . + 0 Parent=13101.m00002
Chr1 MSU_osa1r6 CDS 9232 9244 . + 0 Parent=13101.m00002
Chr1 MSU_osa1r6 CDS 9504 9562 . + 1 Parent=13101.m00002

Thanks!
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