Closed ViriatoII closed 4 years ago
Hi Ricardo
Maria
Thanks!
Have a nice day, Ricardo
Good morning @MariaNattestad ,
Coming back to the output bed file, how do I make sense of the coordinates, sizes and gap sizes?
For example, here I have:
ref_start | ref_end | size | type | ref_gap_size | query_gap_size |
---|---|---|---|---|---|
11616437 | 11621053 | 390 | Repeat_contraction | 4616 | 4226 |
109161822 | 109163268 | 108 | Repeat_expansion | 1446 | 1554 |
So :
ref_start - ref_end = ref_gap_size
and
ref_gap_size - query_gap_size = size
What does this mean for my called SVs? Where do the SV actually start and end? And why are these gap sizes in the picture?
Thank you, Ricardo
The alignments look something like this for repeat contractions and expansions: (from Assemblytics paper main text) The information in the file is describing the gap between those two alignments both from the perspective of the reference (i.e. ref_start, ref_end, and ref_gap_size) and of the query. So you ask where your SVs actually start and end. The simplest answer is just the ref_start and ref_end. But the extra information is there to give you more context.
Thank you once more! I'll read the paper more thoroughfully. Have a nice day.
Hi!
Thank you very much for your software! I'm trying to understand the output bed file I generate (I'm running Assemblytics through Ragoo), particularly the last 3 columns: method query_gap_ovlp ref_gap_ovlp
1) What does it mean to be between alignments and within alignment?
2) What exactly is the gap overlap? In my case I expected ref gap overlap to be higher, since my reference has Ns (gaps), but this is always 0. On the other hand, my query is pacbio reads without Ns, but the query gap overlap varies between 0 and 0.4
3) What is query ID, is it Chr0_RaGOO in my case?
cat assemblytics_out.Assemblytics_structural_variants.bed
Kind regards, Ricardo