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Hi Dr Jiang.
I work with species, genome of which has a high number of genome rearrangements. Because of that I can assembly only diploid version of genome with Flye. And I think, I can resolve the…
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Hi,
1) after doing multiple genome alignment (reference, A, B, C and D genome). I want to know the information of SNP and SV in the alignment compared with the reference genome position(like vcf …
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when I use a vcf with structure variation, It's warning skip Indel site, there are total skip Indel sites number is : 618346,after filter Remain SNP Number : 0. Does it mean that VCF files with struc…
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Hi,
When I get the clustalw.out.checked.filtered.structure file, how can I do statistics for it? For example, the number of gene with large structural variations.
Thanks a lot!
Regards,
…
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I'd like to include the Long-read assemblies file when identifying structural variations.How do I get Long-read assemblies SVS_VCF files?
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After detecting structural variations (SVs) using the default parameters of CuteSV, I found that the bases of “REF” in some INS (insertion) events in the vcf do not match those in the reference genom…
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Hi,
In the paper [Novel sequences, structural variations and gene presence variations of Asian cultivated rice](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5931083/#__sec9title) authors run novoBr…
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Hi,
I am using bcftools 1.15.1. I want to add INFO for a vcf file of structural variations.
The vcf is like:
```
chr1 10627 ID1 N . PASS some_INFO
chr1 90238 ID2 N . PASS some_INFO
chr1 9033…
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Hi, thankyou for the amazing set of tools!
I am calling structural variations using GRIDSS, for that I first used SvPrep, then GRIDSS followed by GRIPSS. Then later, I used files generated by GRIPS…
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Dear Tobias,
I hope this message finds you well.
I am currently engaged in a project that involves tracking the insertion sites of a transgene in the mouse genome. The transgene in question is ap…