User: rob234king

gravatar for rob234king
rob234king580
Reputation:
580
Status:
Trusted
Location:
UK/Harpenden/Rothamsted Research
Website:
http://elvis.misc.cran...
Last seen:
2 weeks, 5 days ago
Joined:
6 years, 9 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 • 167 results • page 1 of 17 • next >
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awk gff column change
... I have had to split by fasta genome into chunks to speed up annotation using maker as we did not have mpi up and chromosomes were very large. I need to add the last value in the string of the first column to columns 4 and 5 to correct the starting and finish positions. I need to do this to multiple ...
gff awk written 9 weeks ago by rob234king580 • updated 9 weeks ago by yztxwd290
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Comment: C: Polish PacBio assembly with Hi-C reads
... how did it go, I was thinking the same? ...
written 10 weeks ago by rob234king580
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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 4 months 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 6 months 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 7 months ago by rob234king580
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Comment: C: remove UTR annotations from gff
... great thanks, I'll give it a go ...
written 7 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 7 months ago by rob234king580 • updated 7 months ago by Ace70
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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 14 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 17 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 18 months ago by rob234king580

Latest awards to rob234king

Popular Question 29 days ago, created a question with more than 1,000 views. For R/perl/python script to bin scaffold coverage by cM for many samples
Popular Question 3 months ago, created a question with more than 1,000 views. For start codon gff annotation corrections using fasta file
Popular Question 4 months ago, created a question with more than 1,000 views. For start codon gff annotation corrections using fasta file
Popular Question 6 months ago, created a question with more than 1,000 views. For start codon gff annotation corrections using fasta file
Great Question 6 months ago, created a question with more than 5,000 views. For Samtools Mpileup Snp Calling Improperly Paired Reads
Popular Question 6 months ago, created a question with more than 1,000 views. For start codon gff annotation corrections using fasta file
Popular Question 13 months ago, created a question with more than 1,000 views. For start codon gff annotation corrections using fasta file
Popular Question 13 months ago, created a question with more than 1,000 views. For How to produce a hom/het snp frequency table
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Workflow Or Tutorial For Snp Calling?
Popular Question 15 months ago, created a question with more than 1,000 views. For start codon gff annotation corrections using fasta file
Popular Question 21 months ago, created a question with more than 1,000 views. For start codon gff annotation corrections using fasta file
Popular Question 2.4 years ago, created a question with more than 1,000 views. For scripting problem to change string match of one file to another
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Appreciated 2.9 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 3.4 years ago, created a question with more than 5,000 views. For New Free Community Tutorial Website For Bioinformatics Learning

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