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

gooday23 · 04-11-2013, 05:32 AM

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!

d1antho · 04-11-2013, 06:01 AM

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!).

aggp11 · 04-11-2013, 06:36 AM

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!

gooday23 · 04-12-2013, 04:19 AM

Thank you~ I will have a try~

gooday23 · 04-12-2013, 04:19 AM

It works really well. Thanks!

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04-11-2013, 05:32 AM	#1
gooday23 Junior Member Location: UK Join Date: Feb 2012 Posts: 3	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!

04-11-2013, 06:01 AM	#2
d1antho Member Location: Ireland Join Date: Mar 2012 Posts: 15	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!).

04-11-2013, 06:36 AM	#3
aggp11 Member Location: Wisconsin Join Date: Jun 2011 Posts: 87	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!

04-12-2013, 04:19 AM	#4
gooday23 Junior Member Location: UK Join Date: Feb 2012 Posts: 3	Thank you~ I will have a try~