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bed file for bacterial rRNA

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.

Thanks

rna-seq
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updated by GenoMax GenoMax • written by kanwarjag kanwarjag

1 answer

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
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written by GenoMax GenoMax

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