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Target intervals for exome
So I'm using target regions from the Roche Nimblegen website on SeqCap_EZ_Exome_v3. I used the capture regions file (SeqCap_EZ_Exome_v3_capture.bed) as the target file for use with analysis software. Looking back, should I have created a buffer around these regions to use as target intervals?
Here is the description from the website about what the capture file includes: "SeqCap_EZ_Exome_v3_capture.bed: This file contains capture target intervals along with associated annotation IDs in BED format. The coordinates listed here correspond to locations where capture probes were actually designed and placed. If an exon was originally targeted for capture, but probes could not be placed in that region (for example, due to highly repetitive sequences), then the coordinates would be included in the SeqCap_EZ_Exome_v3_primary.bed file but not included in the SeqCap_EZ_Exome_v3_capture.bed file. "
Does anyone have any experience with this?