User: rob234king
rob234king • 580
- Reputation:
- 580
- Status:
- Trusted
- Location:
- UK/Harpenden/Rothamsted Research
- Website:
- http://elvis.misc.cran...
- Last seen:
- 5 days ago
- Joined:
- 6 years, 5 months ago
- Email:
- r*********@gmail.com
Cranfield University MSc Applied Bioinformatics, Queen Mary University of London PhD Cancer Radiopharmaceuticals. Employed at Rothamsted Research.
Posts by rob234king
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... I have run Hapcut2 and have a VCF file. I can't see in the VCF where it has assigned the snp to one haplotype or the other, any ideas where that information is kept? I can see it in the other hapcut output file but not the VCF which seems wrong. I assume can separate the two haplotypes in vcf to two ...
written 11 days ago by
rob234king • 580
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... I have a genome expected to be ~400Mbp-800Mbp (I think 800 is with both haplotypes represented) and I have approx 350x pacbio coverage using new sequel II system. I have used Flye and have a reasonable assembly of 4000 contigs with 22Mbp largest scaffold with one gap but I should do better with Falc ...
written 9 weeks ago by
rob234king • 580
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C: remove UTR annotations from gff
... It worked perfectly, once I had the right perl version running for it. ...
written 3 months ago by
rob234king • 580
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Comment:
C: remove UTR annotations from gff
... great thanks, I'll give it a go ...
written 3 months ago by
rob234king • 580
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... I have UTR annotations which I need to remove for a set of genes, which I could do just by deleting but then it would not update the start and stop positions of the gene and mRNA features, and correct exon features. Is there a tool to remove UTR features from a gff file and make the necessary correc ...
written 3 months ago by
rob234king • 580
• updated
3 months ago by
Ace • 60
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Comment:
A: merging 10X genomics assemblies
... didn't try it in the end as got some long reads to do hybrid assembly anyway. surprised there were some snps in 10X assemblies that were mistakes too. ...
written 10 months ago by
rob234king • 580
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Answer:
A: for extension of gene family
... orthomcl all the proteins and see if those you know have additional included in orthomcl. google orthomcl and can use web version or download ...
written 13 months ago by
rob234king • 580
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579
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... I will give CAMSA a go which looks like might do what I want and update but any other ideas, please let me know
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1919-y
...
written 14 months ago by
rob234king • 580
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Comment:
C: merging 10X genomics assemblies
... from the 10X stats which don't match a perl script I have in terms of size of genome etc, but ignoring that, the assembly is better in terms of assembling more but consequently the N50 goes down. However when go beyond numbers and look at genes then there is some variation in terms of scaffolding wh ...
written 14 months ago by
rob234king • 580
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... I have different 10X genomics data assemblies using different subsets of reads with supernova 2.01. We have what should be the best assembly with ideal x42 but when I look at some genes, one of the subset read assemblies will have the missing contig placed for one gene that was missed in the best as ...
written 14 months ago by
rob234king • 580
• updated
6 months ago by
harish • 230
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