For some elements of the file unix_sort_4column_xgen_targets.bed, only one exon from the file sort_gene_exon.genecode.bed overlaps that element, and so one exon ID is reported.
For other elements of the file unix_sort_4column_xgen_targets.bed, two exons from the file sort_gene_exon.genecode.bed overlap that element, and so two exon IDs are reported.
Because you use the --skip-unmapped option, elements from unix_sort_4column_xgen_targets.bed that have zero overlaps with elements from sort_gene_exon.genecode.bed are not reported in the output file. You are skipping unmapped reference elements.
exon 1 and exon 14 are pulled down by the capture probe? Thank you :).
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updated 18 months ago by
Ram
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written 8.5 years ago by
bioguy24
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If the regions of exons 1 and 14 overlap that reference element, then yes. If you're not sure about your input data, do spot checks of specific elements. Also make sure that you are using BEDOPS sort-bed to sort your BED files, because 1) Unix sort is slower and 2) most uses of sort I see on this site do not sort on the third column, while sort-bed does.
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exon 1 and exon 14 are pulled down by the capture probe? Thank you :).
If the regions of exons 1 and 14 overlap that reference element, then yes. If you're not sure about your input data, do spot checks of specific elements. Also make sure that you are using BEDOPS sort-bed to sort your BED files, because 1) Unix sort is slower and 2) most uses of sort I see on this site do not sort on the third column, while sort-bed does.
Thank you :).