Please find the the gff file I have used at this url ftp://ftp.ncbi.nlm.nih.gov/genomes/B.../NC_004556.gff
otherwise also please check a sample of it, hope it will be readable in the post
I am looking for the count of all the reads mapped to each gene. Please let me know if it is correct way I am doing using locus_tag and CDs. It is also microbial genome.
Thank you
otherwise also please check a sample of it, hope it will be readable in the post
##gff-version 3
#!gff-spec-version 1.14
#!source-version NCBI C++ formatter 0.2
##Type DNA NC_004556.1
NC_004556.1 RefSeq source 1 2519802 . + . organism=Xylella fastidiosa Temecula1;mol_type=genomic DNA;strain=Temecula1;db_xref=taxon:183190;note=Pierce%27s disease strain
NC_004556.1 RefSeq gene 146 1465 . + . ID=NC_004556.1:dnaA;locus_tag=PD0001;db_xref=GeneID:1144259
NC_004556.1 RefSeq CDS 146 1462 . + 0 ID=NC_004556.1:dnaA:unknown_transcript_1;Parent=NC_004556.1:dnaA;locus_tag=PD0001;note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;transl_table=11;product=chromosomal replication initiation protein;protein_id=NP_778260.1;db_xref=GI:28197946;db_xref=GeneID:1144259;exon_number=1
NC_004556.1 RefSeq start_codon 146 148 . + 0 ID=NC_004556.1:dnaA:unknown_transcript_1;Parent=NC_004556.1:dnaA;locus_tag=PD0001;note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;transl_table=11;product=chromosomal replication initiation protein;protein_id=NP_778260.1;db_xref=GI:28197946;db_xref=GeneID:1144259;exon_number=1
NC_004556.1 RefSeq stop_codon 1463 1465 . + 0 ID=NC_004556.1:dnaA:unknown_transcript_1;Parent=NC_004556.1:dnaA;locus_tag=PD0001;note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;transl_table=11;product=chromosomal replication initiation protein;protein_id=NP_778260.1;db_xref=GI:28197946;db_xref=GeneID:1144259;exon_number=1
NC_004556.1 RefSeq gene 1747 2847 . + . ID=NC_004556.1:dnaN;locus_tag=PD0002;db_xref=GeneID:1144260
NC_004556.1 RefSeq CDS 1747 2844 . + 0 ID=NC_004556.1:dnaN:unknown_transcript_1;Parent=NC_004556.1:dnaN;locus_tag=PD0002;EC_number=2.7.7.7;note=binds the polymerase to DNA and acts as a sliding clamp;transl_table=11;product=DNA polymerase III subunit beta;protein_id=NP_778261.1;db_xref=GI:28197947;db_xref=GeneID:1144260;exon_number=1
NC_004556.1 RefSeq start_codon 1747 1749 . + 0 ID=NC_004556.1:dnaN:unknown_transcript_1;Parent=NC_004556.1:dnaN;locus_tag=PD0002;EC_number=2.7.7.7;note=binds the polymerase to DNA and acts as a sliding clamp;transl_table=11;product=DNA polymerase III subunit beta;protein_id=NP_778261.1;db_xref=GI:28197947;db_xref=GeneID:1144260;exon_number=1
NC_004556.1 RefSeq stop_codon 2845 2847 . + 0 ID=NC_004556.1:dnaN:unknown_transcript_1;Parent=NC_004556.1:dnaN;locus_tag=PD0002;EC_number=2.7.7.7;note=binds the polymerase to DNA and acts as a sliding clamp;transl_table=11;product=DNA polymerase III subunit beta;protein_id=NP_778261.1;db_xref=GI:28197947;db_xref=GeneID:1144260;exon_number=1
NC_004556.1 RefSeq gene 3153 4247 . + . ID=NC_004556.1:recF;locus_tag=PD0003;gene_synonym=uvrF;db_xref=GeneID:1144261
NC_004556.1 RefSeq CDS 3153 4244 . + 0 ID=NC_004556.1:recF:unknown_transcript_1;Parent=NC_004556.1:recF;locus_tag=PD0003;gene_synonym=uvrF;note=Required for DNA replication%3B binds preferentially to single-stranded%2C linear DNA;transl_table=11;product=recombination protein F;protein_id=NP_778262.1;db_xref=GI:28197948;db_xref=GeneID:1144261;exon_number=1
NC_004556.1 RefSeq start_codon 3153 3155 . + 0 ID=NC_004556.1:recF:unknown_transcript_1;Parent=NC_004556.1:recF;locus_tag=PD0003;gene_synonym=uvrF;note=Required for DNA replication%3B binds preferentially to single-stranded%2C linear DNA;transl_table=11;product=recombination protein F;protein_id=NP_778262.1;db_xref=GI:28197948;db_xref=GeneID:1144261;exon_number=1
NC_004556.1 RefSeq stop_codon 4245 4247 . + 0 ID=NC_004556.1:recF:unknown_transcript_1;Parent=NC_004556.1:recF;locus_tag=PD0003;gene_synonym=uvrF;note=Required for DNA replication%3B binds preferentially to single-stranded%2C linear DNA;transl_table=11;product=recombination protein F;protein_id=NP_778262.1;db_xref=GI:28197948;db_xref=GeneID:1144261;exon_number=1
#!gff-spec-version 1.14
#!source-version NCBI C++ formatter 0.2
##Type DNA NC_004556.1
NC_004556.1 RefSeq source 1 2519802 . + . organism=Xylella fastidiosa Temecula1;mol_type=genomic DNA;strain=Temecula1;db_xref=taxon:183190;note=Pierce%27s disease strain
NC_004556.1 RefSeq gene 146 1465 . + . ID=NC_004556.1:dnaA;locus_tag=PD0001;db_xref=GeneID:1144259
NC_004556.1 RefSeq CDS 146 1462 . + 0 ID=NC_004556.1:dnaA:unknown_transcript_1;Parent=NC_004556.1:dnaA;locus_tag=PD0001;note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;transl_table=11;product=chromosomal replication initiation protein;protein_id=NP_778260.1;db_xref=GI:28197946;db_xref=GeneID:1144259;exon_number=1
NC_004556.1 RefSeq start_codon 146 148 . + 0 ID=NC_004556.1:dnaA:unknown_transcript_1;Parent=NC_004556.1:dnaA;locus_tag=PD0001;note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;transl_table=11;product=chromosomal replication initiation protein;protein_id=NP_778260.1;db_xref=GI:28197946;db_xref=GeneID:1144259;exon_number=1
NC_004556.1 RefSeq stop_codon 1463 1465 . + 0 ID=NC_004556.1:dnaA:unknown_transcript_1;Parent=NC_004556.1:dnaA;locus_tag=PD0001;note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;transl_table=11;product=chromosomal replication initiation protein;protein_id=NP_778260.1;db_xref=GI:28197946;db_xref=GeneID:1144259;exon_number=1
NC_004556.1 RefSeq gene 1747 2847 . + . ID=NC_004556.1:dnaN;locus_tag=PD0002;db_xref=GeneID:1144260
NC_004556.1 RefSeq CDS 1747 2844 . + 0 ID=NC_004556.1:dnaN:unknown_transcript_1;Parent=NC_004556.1:dnaN;locus_tag=PD0002;EC_number=2.7.7.7;note=binds the polymerase to DNA and acts as a sliding clamp;transl_table=11;product=DNA polymerase III subunit beta;protein_id=NP_778261.1;db_xref=GI:28197947;db_xref=GeneID:1144260;exon_number=1
NC_004556.1 RefSeq start_codon 1747 1749 . + 0 ID=NC_004556.1:dnaN:unknown_transcript_1;Parent=NC_004556.1:dnaN;locus_tag=PD0002;EC_number=2.7.7.7;note=binds the polymerase to DNA and acts as a sliding clamp;transl_table=11;product=DNA polymerase III subunit beta;protein_id=NP_778261.1;db_xref=GI:28197947;db_xref=GeneID:1144260;exon_number=1
NC_004556.1 RefSeq stop_codon 2845 2847 . + 0 ID=NC_004556.1:dnaN:unknown_transcript_1;Parent=NC_004556.1:dnaN;locus_tag=PD0002;EC_number=2.7.7.7;note=binds the polymerase to DNA and acts as a sliding clamp;transl_table=11;product=DNA polymerase III subunit beta;protein_id=NP_778261.1;db_xref=GI:28197947;db_xref=GeneID:1144260;exon_number=1
NC_004556.1 RefSeq gene 3153 4247 . + . ID=NC_004556.1:recF;locus_tag=PD0003;gene_synonym=uvrF;db_xref=GeneID:1144261
NC_004556.1 RefSeq CDS 3153 4244 . + 0 ID=NC_004556.1:recF:unknown_transcript_1;Parent=NC_004556.1:recF;locus_tag=PD0003;gene_synonym=uvrF;note=Required for DNA replication%3B binds preferentially to single-stranded%2C linear DNA;transl_table=11;product=recombination protein F;protein_id=NP_778262.1;db_xref=GI:28197948;db_xref=GeneID:1144261;exon_number=1
NC_004556.1 RefSeq start_codon 3153 3155 . + 0 ID=NC_004556.1:recF:unknown_transcript_1;Parent=NC_004556.1:recF;locus_tag=PD0003;gene_synonym=uvrF;note=Required for DNA replication%3B binds preferentially to single-stranded%2C linear DNA;transl_table=11;product=recombination protein F;protein_id=NP_778262.1;db_xref=GI:28197948;db_xref=GeneID:1144261;exon_number=1
NC_004556.1 RefSeq stop_codon 4245 4247 . + 0 ID=NC_004556.1:recF:unknown_transcript_1;Parent=NC_004556.1:recF;locus_tag=PD0003;gene_synonym=uvrF;note=Required for DNA replication%3B binds preferentially to single-stranded%2C linear DNA;transl_table=11;product=recombination protein F;protein_id=NP_778262.1;db_xref=GI:28197948;db_xref=GeneID:1144261;exon_number=1
Thank you
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