Agilent Sure Select .bed file v6 and v8

Question

[Vaishnavi]

Hi, I would like to differentiate between the Agilent SureSelect .bed file version v6 & v8. The release notes is unclear and couldn't arrive at any inference. I would like to differentiate and get the genomic regions and gene names as a separate .bed file comparing both the versions. Kindly help.

[ATpoint]

If it is BED files then use any of the bedtools operations to find overlaps and differences, e.g. intersect.

[Vaishnavi]

I tried doing it, but 6k+ rows in my bed file returned "-" in the place of gene regions. I've created those regions as a separate .bed file. I would like to annotate those regions alone in the file with gene names. Any lead would be helpful.

[ATpoint]

Without code or data help is close to impossible, please add something to work with.

[Vaishnavi]

I annotated the Agilent SureSelect bed file v6 with refFlat.txt which returned a bed file with gene names annotated, which looked something like this

Chr Start End Gene

chr1 12080 12251 DDX11L17,DDX11L1

chr1 12595 12802 DDX11L17,DDX11L1

chr1 13163 13658 DDX11L17,DDX11L1

chr1 14620 15015 WASH7P

chr1 15795 15914 WASH7P

chr1 16743 17098 WASH7P

chr1 17247 18121 WASH7P,MIR6859-1,MIR6859-2,MIR6859-3,MIR6859-4

chr1 18216 18411 WASH7P

I intersected v6.bed with v8.bed to pull out the common region. using the code

$ bedtools intersect -a v6.bed -b v8.bed -f 1 > results.bed

but i could notice that there are some regions in the bed file that had no gene names and the bed file looked like this after filtering out those regions alone

Chr Start End Gene

chr1 65509 65726 -

chr1 65776 65972 -

chr1 120817 120937 -

chr1 129075 129255 -

chr1 228399 228603 -

chr1 228681 228801 -

chr1 267138 267258 -

chr1 320927 321232 -

So now, i would like to annotate these regions alone with gene names. Help!!