I am trying to get rRNA bed file from USCS browser @http://microbes.ucsc.edu/cgi-bin/hgTables?hgsid=1455159&clade=bacteria-gammaproteobacteria&org=Escherichia+coli+K12&db=eschColi_K12&hgta_group=genes&hgta_track=tRNAs&hgta_table=0&hgta_regionType=genome&position=chr%3A10001-35000&hgta_outputType=bed&hgta_outFileName=E_coli_K12
However I could not figure out how I can get rRNA coordinates in E Coli K12 (bacterial) genome.
You should be able to find that information in the GFF file. I am linking Ensembl's version here.
grep rRNA_gene Escherichia_coli_k_12_gca_000981485.EcoliK12AG100.34.chromosome.I.gff3 | more
I ena rRNA_gene 223939 225480 . + . ID=gene:EBG00001511392;Name=rrsH;biotype=rRNA;gene_id=EBG00001511392;logic_name=ena_rna
I ena rRNA_gene 225927 228830 . + . ID=gene:EBG00001511314;Name=rrlH;biotype=rRNA;gene_id=EBG00001511314;logic_name=ena_rna
I ena rRNA_gene 228924 229043 . + . ID=gene:EBG00001511364;Name=rrfH;biotype=rRNA;gene_id=EBG00001511364;logic_name=ena_rna
I ena rRNA_gene 2722373 2722492 . - . ID=gene:EBG00001511372;Name=rrfG;biotype=rRNA;gene_id=EBG00001511372;logic_name=ena_rna
I ena rRNA_gene 2722585 2725488 . - . ID=gene:EBG00001511386;Name=rrlG;biotype=rRNA;gene_id=EBG00001511386;logic_name=ena_rna
I ena rRNA_gene 2725920 2727461 . - . ID=gene:EBG00001511322;Name=rrsG;biotype=rRNA;gene_id=EBG00001511322;logic_name=ena_rna
I ena rRNA_gene 3419935 3420054 . - . ID=gene:EBG00001511363;Name=rrfF;biotype=rRNA;gene_id=EBG00001511363;logic_name=ena_rna
I ena rRNA_gene 3420180 3420299 . - . ID=gene:EBG00001511403;Name=rrfD;biotype=rRNA;gene_id=EBG00001511403;logic_name=ena_rna
I ena rRNA_gene 3420392 3423295 . - . ID=gene:EBG00001511425;Name=rrlD;biotype=rRNA;gene_id=EBG00001511425;logic_name=ena_rna
I ena rRNA_gene 3423733 3425274 . - . ID=gene:EBG00001511350;Name=rrsD;biotype=rRNA;gene_id=EBG00001511350;logic_name=ena_rna
I ena rRNA_gene 3938320 3939861 . + . ID=gene:EBG00001511437;Name=rrsC;biotype=rRNA;gene_id=EBG00001511437;logic_name=ena_rna
I ena rRNA_gene 3940216 3943080 . + . ID=gene:EBG00001511360;Name=rrlC;biotype=rRNA;gene_id=EBG00001511360;logic_name=ena_rna
I ena rRNA_gene 3943173 3943292 . + . ID=gene:EBG00001511332;Name=rrfC;biotype=rRNA;gene_id=EBG00001511332;logic_name=ena_rna
I ena rRNA_gene 4032045 4033586 . + . ID=gene:EBG00001511326;Name=rrsA;biotype=rRNA;gene_id=EBG00001511326;logic_name=ena_rna
I ena rRNA_gene 4034033 4036937 . + . ID=gene:EBG00001511291;Name=rrlA;biotype=rRNA;gene_id=EBG00001511291;logic_name=ena_rna
I ena rRNA_gene 4037031 4037150 . + . ID=gene:EBG00001511419;Name=rrfA;biotype=rRNA;gene_id=EBG00001511419;logic_name=ena_rna
I ena rRNA_gene 4163132 4164673 . + . ID=gene:EBG00001511446;Name=rrsB;biotype=rRNA;gene_id=EBG00001511446;logic_name=ena_rna
I ena rRNA_gene 4165114 4168017 . + . ID=gene:EBG00001511356;Name=rrlB;biotype=rRNA;gene_id=EBG00001511356;logic_name=ena_rna
I ena rRNA_gene 4168110 4168229 . + . ID=gene:EBG00001511349;Name=rrfB;biotype=rRNA;gene_id=EBG00001511349;logic_name=ena_rna
I ena rRNA_gene 4204620 4206161 . + . ID=gene:EBG00001511406;Name=rrsE;biotype=rRNA;gene_id=EBG00001511406;logic_name=ena_rna
I ena rRNA_gene 4206516 4209419 . + . ID=gene:EBG00001511290;Name=rrlE;biotype=rRNA;gene_id=EBG00001511290;logic_name=ena_rna
I ena rRNA_gene 4209513 4209632 . + . ID=gene:EBG00001511377;Name=rrfE;biotype=rRNA;gene_id=EBG00001511377;logic_name=ena_rna
OR
grep rRNA_gene Escherichia_coli_k_12_gca_000981485.EcoliK12AG100.34.chromosome.I.gff3 | awk '{print $1"\t"$4"\t"$5}'
I 223939 225480
I 225927 228830
I 228924 229043
I 2722373 2722492
I 2722585 2725488
I 2725920 2727461
I 3419935 3420054
I 3420180 3420299
I 3420392 3423295
I 3423733 3425274
I 3938320 3939861
I 3940216 3943080
I 3943173 3943292
I 4032045 4033586
I 4034033 4036937
I 4037031 4037150
I 4163132 4164673
I 4165114 4168017
I 4168110 4168229
I 4204620 4206161
I 4206516 4209419
I 4209513 4209632
