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  • Downloading UCSC annotation files

    Hello,

    Do you know maybe how to download the UCSC annotation files (with genomes of Campylobacter jejuni, Campylobacter jejuni 81-176, Campylobacter jejuni RM1221) from UCSC browser?

  • #2
    I don't think the microbial UCSC genome browser allows downloads of data (like the regular UCSC browser does). You should check @NCBI (e.g. https://www.ncbi.nlm.nih.gov/genome/149).

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    • #3
      Dwonloading annotation files from UCSC browser?

      Thanks for quick answer.
      Do you know how to download the annotation files from regular UCSC browser?

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      • #4
        Download links for genomes are at: http://hgdownload.soe.ucsc.edu/downloads.html

        There are links for annotation database once you select an organism (above link only has eukaryotes and a few exceptional genomes but no bacteria).

        If you need GTF/GFF format then use the "Table browser" tool.

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        • #5
          Yikes. I actually didn't expect it to work ... but ...

          This script ~seems~ to work ...

          #!/bin/sh
          POSITION="chr:1-1641481"
          wget --progress=dot \
          'http://microbes.ucsc.edu/cgi-bin/hgTables?db=campJeju&hgta_compressType=none&'\
          'hgta_group=genes&hgta_outputType=gff&outGff=1&hgta_regionType=range&'\
          'hgta_table=refSeq&hgta_track=refSeq&org=Campylobacter&position='${POSITION}\
          '&submit=submit&hgta_doTopSubmit=1' \
          -O genscan.${POSITION}.gtf


          Hack the fields to get the table you want; i.e "db" which is the organism code, "hgta_table" for the annontation table, etc. Also, can probably make the positionrange really big rather than precise genome size.

          I can't vouch for the output ;check that it is doing the right thing,
          but it looks like this ...

          head genscan.chr\:1-1641481.gtf
          chr campJeju_refSeq start_codon 1 3 1.000000 + . gene_id "Cj0001"; transcript_id "Cj0001";
          chr campJeju_refSeq CDS 1 1320 1.000000 + 0 gene_id "Cj0001"; transcript_id "Cj0001";
          chr campJeju_refSeq stop_codon 1321 1323 1.000000 + . gene_id "Cj0001"; transcript_id "Cj0001";
          chr campJeju_refSeq exon 1 1323 1.000000 + . gene_id "Cj0001"; transcript_id "Cj0001";
          chr campJeju_refSeq start_codon 1483 1485 2.000000 + . gene_id "Cj0002"; transcript_id "Cj0002";
          chr campJeju_refSeq CDS 1483 2547 2.000000 + 0 gene_id "Cj0002"; transcript_id "Cj0002";
          chr campJeju_refSeq stop_codon 2548 2550 2.000000 + . gene_id "Cj0002"; transcript_id "Cj0002";
          chr campJeju_refSeq exon 1483 2550 2.000000 + . gene_id "Cj0002"; transcript_id "Cj0002";
          chr campJeju_refSeq start_codon 2579 2581 3.000000 + . gene_id "Cj0003"; transcript_id "Cj0003";
          chr campJeju_refSeq CDS 2579 4885 3.000000 + 0 gene_id "Cj0003"; transcript_id "Cj0003



          It looks like the separate microbial genomes site at UCSC uses the same "table browser" code as the regular UCSC site. There might be a way to use a mysql client to snag the data, too.
          Last edited by Richard Finney; 04-11-2016, 09:58 AM.

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          • #6
            Thanks so much!

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            • #7
              Wow, that's really great!!! Wonderful!

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