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Old 07-14-2011, 05:30 AM   #1
kellogg
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Default Illumina Whole Exome coverage

Before I send some samples off for whole exome sequencing is there a way to check the coverage of the region that I'm interested in?

Ideally a track on UCSC genome browser or the Savant genome browser would be great.

Thanks
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Old 07-14-2011, 06:34 AM   #2
epistatic
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I like to load the BED file of the capture probes in IGV and take a look.

If you go to Illumina's iCom site, go to downloads and do a .bed search. Download the following, you can load into UCSC, Savant, IGV, etc. and take a look.

TruSeq Exome Targeted Regions BED file

This gzipped file (TruSeq_exome_targeted_regions.hg19.chr.bed.gz) contains information on the Targeted Exons in the TruSeq Exome product (201,071 regions). It can be loaded into UCSC Genome Browser to visualize specific target regions or to compare with other data of interest accesible via UCSC Browser's tables function. This BED file has 6 columns 1 chromosome 2 chromStart (zero-based) first position of the feature 3 chromEnd (zero-based) first position after the feature 4 name (chromosome:chromStart-chromEnd:gene) 5 length (chromEnd-chromStart) 6 strand (all targets mapped to the plus strand = +)
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Old 07-14-2011, 06:46 AM   #3
kellogg
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Thanks for the suggestion, but to get the data from the iCom site you need an account, and you can't seem to get an account without previously placing an order.

Is the BED file available on a FTP somewhere?

Thanks

Quote:
Originally Posted by epistatic View Post
I like to load the BED file of the capture probes in IGV and take a look.

If you go to Illumina's iCom site, go to downloads and do a .bed search. Download the following, you can load into UCSC, Savant, IGV, etc. and take a look.

TruSeq Exome Targeted Regions BED file

This gzipped file (TruSeq_exome_targeted_regions.hg19.chr.bed.gz) contains information on the Targeted Exons in the TruSeq Exome product (201,071 regions). It can be loaded into UCSC Genome Browser to visualize specific target regions or to compare with other data of interest accesible via UCSC Browser's tables function. This BED file has 6 columns 1 chromosome 2 chromStart (zero-based) first position of the feature 3 chromEnd (zero-based) first position after the feature 4 name (chromosome:chromStart-chromEnd:gene) 5 length (chromEnd-chromStart) 6 strand (all targets mapped to the plus strand = +)
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Old 07-14-2011, 08:01 AM   #4
epistatic
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http://dl.dropbox.com/u/30955182/Tru...ns-BED-file.gz
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Old 07-14-2011, 08:03 AM   #5
kellogg
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Thanks for the link

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Old 07-14-2011, 10:18 AM   #6
kellogg
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Now that I have the Illumina whole exome BED file and a BED file of the region of interest, is there a way to get the computer to subtract one from the other to give me regions that are coding but not covered by the Illumina data?
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