Hi All,
I have a problem in counting reads using HTSe-count. The error is like,
csg@csg-W650EH:~/Downloads$ python -m HTSeq.scripts.count Nipponbare_ref_assembly.sam chr1.gff3
Error occured in line 3 of file chr1.gff3.
Error: Feature LOC_Os01g01010.1:exon_1 does not contain a 'gene_id' attribute
[Exception type: SystemExit, raised in count.py:55]
csg@csg-W650EH:~/Downloads$
Following is a portion of the gff3 file,
##gff-version 3
Chr1 MSU_osa1r7 mRNA 2903 10817 . + . ID=LOC_Os01g01010.1;Name=LOC_Os01g01010.1;Parent=LOC_Os01g01010
Chr1 MSU_osa1r7 exon 2903 3268 . + . ID=LOC_Os01g01010.1:exon_1;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 exon 3354 3616 . + . ID=LOC_Os01g01010.1:exon_2;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 exon 4357 4455 . + . ID=LOC_Os01g01010.1:exon_3;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 exon 5457 5560 . + . ID=LOC_Os01g01010.1:exon_4;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 exon 7136 7944 . + . ID=LOC_Os01g01010.1:exon_5;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 exon 8028 8150 . + . ID=LOC_Os01g01010.1:exon_6;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 exon 8232 8320 . + . ID=LOC_Os01g01010.1:exon_7;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 exon 8408 8608 . + . ID=LOC_Os01g01010.1:exon_8;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 exon 9210 9617 . + . ID=LOC_Os01g01010.1:exon_9;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 exon 10104 10187 . + . ID=LOC_Os01g01010.1:exon_10;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 exon 10274 10430 . + . ID=LOC_Os01g01010.1:exon_11;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 exon 10504 10817 . + . ID=LOC_Os01g01010.1:exon_12;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 five_prime_UTR 2903 3268 . + . ID=LOC_Os01g01010.1:utr_1;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 five_prime_UTR 3354 3448 . + . ID=LOC_Os01g01010.1:utr_2;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 CDS 3449 3616 . + . ID=LOC_Os01g01010.1:cds_1;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 CDS 4357 4455 . + . ID=LOC_Os01g01010.1:cds_2;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 CDS 5457 5560 . + . ID=LOC_Os01g01010.1:cds_3;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 CDS 7136 7944 . + . ID=LOC_Os01g01010.1:cds_4;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 CDS 8028 8150 . + . ID=LOC_Os01g01010.1:cds_5;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 CDS 8232 8320 . + . ID=LOC_Os01g01010.1:cds_6;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 CDS 8408 8608 . + . ID=LOC_Os01g01010.1:cds_7;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 CDS 9210 9617 . + . ID=LOC_Os01g01010.1:cds_8;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 CDS 10104 10187 . + . ID=LOC_Os01g01010.1:cds_9;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 CDS 10274 10297 . + . ID=LOC_Os01g01010.1:cds_10;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 three_prime_UTR 10298 10430 . + . ID=LOC_Os01g01010.1:utr_3;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 three_prime_UTR 10504 10817 . + . ID=LOC_Os01g01010.1:utr_4;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 mRNA 2984 10562 . + . ID=LOC_Os01g01010.2;Name=LOC_Os01g01010.2;Parent=LOC_Os01g01010
Chr1 MSU_osa1r7 exon 2984 3255 . + . ID=LOC_Os01g01010.2:exon_1;Parent=LOC_Os01g01010.2
Chr1 MSU_osa1r7 exon 3354 3616 . + . ID=LOC_Os01g01010.2:exon_2;Parent=LOC_Os01g01010.2
Chr1 MSU_osa1r7 exon 4357 4455 . + . ID=LOC_Os01g01010.2:exon_3;Parent=LOC_Os01g01010.2
Kindly consider that I am a fresher in Rna seq data analysis.
Thank you,
anikng
I have a problem in counting reads using HTSe-count. The error is like,
csg@csg-W650EH:~/Downloads$ python -m HTSeq.scripts.count Nipponbare_ref_assembly.sam chr1.gff3
Error occured in line 3 of file chr1.gff3.
Error: Feature LOC_Os01g01010.1:exon_1 does not contain a 'gene_id' attribute
[Exception type: SystemExit, raised in count.py:55]
csg@csg-W650EH:~/Downloads$
Following is a portion of the gff3 file,
##gff-version 3
Chr1 MSU_osa1r7 mRNA 2903 10817 . + . ID=LOC_Os01g01010.1;Name=LOC_Os01g01010.1;Parent=LOC_Os01g01010
Chr1 MSU_osa1r7 exon 2903 3268 . + . ID=LOC_Os01g01010.1:exon_1;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 exon 3354 3616 . + . ID=LOC_Os01g01010.1:exon_2;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 exon 4357 4455 . + . ID=LOC_Os01g01010.1:exon_3;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 exon 5457 5560 . + . ID=LOC_Os01g01010.1:exon_4;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 exon 7136 7944 . + . ID=LOC_Os01g01010.1:exon_5;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 exon 8028 8150 . + . ID=LOC_Os01g01010.1:exon_6;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 exon 8232 8320 . + . ID=LOC_Os01g01010.1:exon_7;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 exon 8408 8608 . + . ID=LOC_Os01g01010.1:exon_8;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 exon 9210 9617 . + . ID=LOC_Os01g01010.1:exon_9;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 exon 10104 10187 . + . ID=LOC_Os01g01010.1:exon_10;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 exon 10274 10430 . + . ID=LOC_Os01g01010.1:exon_11;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 exon 10504 10817 . + . ID=LOC_Os01g01010.1:exon_12;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 five_prime_UTR 2903 3268 . + . ID=LOC_Os01g01010.1:utr_1;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 five_prime_UTR 3354 3448 . + . ID=LOC_Os01g01010.1:utr_2;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 CDS 3449 3616 . + . ID=LOC_Os01g01010.1:cds_1;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 CDS 4357 4455 . + . ID=LOC_Os01g01010.1:cds_2;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 CDS 5457 5560 . + . ID=LOC_Os01g01010.1:cds_3;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 CDS 7136 7944 . + . ID=LOC_Os01g01010.1:cds_4;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 CDS 8028 8150 . + . ID=LOC_Os01g01010.1:cds_5;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 CDS 8232 8320 . + . ID=LOC_Os01g01010.1:cds_6;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 CDS 8408 8608 . + . ID=LOC_Os01g01010.1:cds_7;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 CDS 9210 9617 . + . ID=LOC_Os01g01010.1:cds_8;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 CDS 10104 10187 . + . ID=LOC_Os01g01010.1:cds_9;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 CDS 10274 10297 . + . ID=LOC_Os01g01010.1:cds_10;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 three_prime_UTR 10298 10430 . + . ID=LOC_Os01g01010.1:utr_3;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 three_prime_UTR 10504 10817 . + . ID=LOC_Os01g01010.1:utr_4;Parent=LOC_Os01g01010.1
Chr1 MSU_osa1r7 mRNA 2984 10562 . + . ID=LOC_Os01g01010.2;Name=LOC_Os01g01010.2;Parent=LOC_Os01g01010
Chr1 MSU_osa1r7 exon 2984 3255 . + . ID=LOC_Os01g01010.2:exon_1;Parent=LOC_Os01g01010.2
Chr1 MSU_osa1r7 exon 3354 3616 . + . ID=LOC_Os01g01010.2:exon_2;Parent=LOC_Os01g01010.2
Chr1 MSU_osa1r7 exon 4357 4455 . + . ID=LOC_Os01g01010.2:exon_3;Parent=LOC_Os01g01010.2
Kindly consider that I am a fresher in Rna seq data analysis.
Thank you,
anikng
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