Hi Guys,
I ran SVDetect on Next generation paired end data and got the output but I am confused as to how to interpret the intrachromosomal deletions.
My understanding of the basic deletion meaning is that a part of a chromosome is deleted. However SVDetect gives two coordinates for the deletion position which is confusing to me. Can anyone explain this for me please?
I will give the header and an example of a deletion below:
In this example SVDetect detected a deletion in chromosome 15 apparently at 8996748-8997144 but then it mentions that it was also in the same chromosome at 8997145-8997470.
Header:
chr_type SV_type BAL_type chromosome1 start1-end1 average_dist chromosome2 start2-end2 nb_pairs score_strand_filtering score_order_filtering score_insert_size_filtering final_score breakpoint1_start1-end1 breakpoint2_start2-end2
Deletion:
INTRA DELETION UNBAL chr15 8996748-8997144 416 chr15 8997145-8997470 19 100% 100% 100% 1 8997144-8997130 8997089-8997146
I would greatly appreciate your help as I am trying to wrap up this project now.
-
The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...07-08-2024, 03:19 PM