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  • Any tool can be fed a list of genome locations and output annotations?

    I have a bunch of genome locations and I want to find out what they are. For example, are they located in known genes or non-coding RNA regions or some others. Anyone could suggest me a tool that can be fed in locations and give me a list of annotation?

    Thank you very much!

  • #2
    SNPdat sounds like it would ideal for the task (http://code.google.com/p/snpdat/).

    It simply takes as input a tab-delimited file with chr, genomic location and mutation (If you dont have mutations you can always just set this to A,T,C or G and ignore the sequence annotations if performs). Then you just need an annotation file in GTF and a FASTA file. It will annotate locations/SNPs to any feature in the GTF (such as genes/exons/CDS etc) that contains the location. If your SNP/location occurs outside of a feature it will tell you if it is intergenic or intronic and return information on the nearest features and genes (and more!).

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    • #3
      You could also use intersectBed from Bedtools (http://bedtools.readthedocs.org/en/l...intersect.html). You will need your location BED file (chr, start, stop) and an annotation GTF/GFF/BED file from a source like GENCODE (http://www.gencodegenes.org/releases/15.html)

      Hope this helps!

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      • #4
        Thank you~ I will have a try~

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        • #5
          It works really well. Thanks!

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