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Old 11-27-2013, 05:43 PM   #1
Junior Member
Location: Taiwan

Join Date: Nov 2013
Posts: 4
Default mm9 annotation

Hello all,

I am working on NGS data and want to compare my results with the genomic features. So could any one please help me, how to make an annotation bed file containing information of promoter, exon, introns, intergenic regions, repeates.
I tried it with UCSC table browser but not very sure with the correctness of my table.

Is there any tool is available for this purpose, So there would be less chance of getting wrong file for my further downstream analysis.

Any suggestion regarding this would be highly appreciated.

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Old 11-28-2013, 01:05 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

Have a look at the makeTranscriptDbFromUCSC() function in GenomicFeatures (it's an R/Bioconductor package). You then have functions like exons(), intronsByTranscript(), etc. Though, you might have better luck with just using GenomicRanges, since I kind of doubt that the aforementioned functions will deal with overlapping exons/introns in the way you want.

For repeats, just download the repeatmasker track.
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bioinformatics, chip seq, ngs analysis, rna sequencing

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