User: rob234king

gravatar for rob234king
rob234king580
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

<prev • 165 results • page 1 of 17 • next >
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hapcut2 output and figures
... 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 ...
hapcut2 phasing written 11 days ago by rob234king580
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Sequel II large data set Falcon parameters query
... 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 ...
falcon pacbio written 9 weeks ago by rob234king580
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Comment: C: remove UTR annotations from gff
... It worked perfectly, once I had the right perl version running for it. ...
written 3 months ago by rob234king580
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Comment: C: remove UTR annotations from gff
... great thanks, I'll give it a go ...
written 3 months ago by rob234king580
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remove UTR annotations from gff
... 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 ...
gff written 3 months ago by rob234king580 • updated 3 months ago by Ace60
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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 rob234king580
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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 rob234king580
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Answer: A: merging 10X genomics assemblies
... 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 rob234king580
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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 rob234king580
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merging 10X genomics assemblies
... 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 ...
10x written 14 months ago by rob234king580 • updated 6 months ago by harish230

Latest awards to rob234king

Popular Question 26 days ago, created a question with more than 1,000 views. For start codon gff annotation corrections using fasta file
Popular Question 11 weeks ago, created a question with more than 1,000 views. For start codon gff annotation corrections using fasta file
Popular Question 12 weeks ago, created a question with more than 1,000 views. For start codon gff annotation corrections using fasta file
Great Question 12 weeks ago, created a question with more than 5,000 views. For Samtools Mpileup Snp Calling Improperly Paired Reads
Popular Question 9 months ago, created a question with more than 1,000 views. For How to produce a hom/het snp frequency table
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Workflow Or Tutorial For Snp Calling?
Popular Question 9 months ago, created a question with more than 1,000 views. For start codon gff annotation corrections using fasta file
Popular Question 11 months ago, created a question with more than 1,000 views. For start codon gff annotation corrections using fasta file
Popular Question 17 months ago, created a question with more than 1,000 views. For start codon gff annotation corrections using fasta file
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Popular Question 2.6 years ago, created a question with more than 1,000 views. For Genemark-Es Gtf Output Conversion To Mod
Appreciated 2.6 years ago, created a post with more than 5 votes. For A: How To Remove Common Variants Present In Two Vcf Files?
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Great Question 3.1 years ago, created a question with more than 5,000 views. For New Free Community Tutorial Website For Bioinformatics Learning

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