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Old 04-21-2011, 12:38 PM   #1
Location: USA

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Default "coverage" of introns, intergenic regions for RNASEQ

I would like to determine the % of reads mapping to exons, introns and intergenic regions. I know BEDTools can do this, but I am not sure how to get the GFF files with the information for exons, introns and intergenic regions separately. Any help? Is there a better/easier way?
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Old 04-22-2011, 02:07 PM   #2
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One easy way is through UCSC.

When you go to get the Refseq or UCSC knownGene table in BED format, for example, you can choose to report exons, introns, UTRs, etc.

Some of the tables will not have this information, making your life difficult. Like the Ensembl table in UCSC doesn't have this option as far as I can see.

For Ensembl if you prefer it, the GTF file you can get for their db has useful meta info columns 2 and 3 that can help you do this as well.
Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog]
Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post]
Projects: U87MG whole genome sequence [Website] [Paper]
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Old 09-07-2011, 02:51 PM   #3
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UCSC bed files potentially cause the over-counting problem.
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