User: rob234king

gravatar for rob234king
rob234king560
Reputation:
560
Status:
Trusted
Location:
UK/Harpenden/Rothamsted Research
Website:
http://elvis.misc.cran...
Last seen:
21 hours ago
Joined:
5 years, 4 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 • 159 results • page 1 of 16 • next >
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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 9 days ago by rob234king560
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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 4 weeks ago by rob234king560
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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 4 weeks ago by rob234king560
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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 4 weeks ago by rob234king560
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Comment: C: script for task or AWK
... I can do this last bit in excel. Thanks this saved me so much time trying to get a perl script to dot he same! ...
written 9 weeks ago by rob234king560
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Comment: C: script for task or AWK
... I would only need the lead chromosome for each so below. Guess then for each sequence I could take the highest value in the end column some how. seq000001 Fc06 35.948-51.086 72 seq000002 Fc09 13.078-39.857 34 ...
written 9 weeks ago by rob234king560
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Comment: C: script for task or AWK
... damn, that easy? I'll download datamash, will it also report how many markers there were, I made a change to what I was looking for above but already something to work with. thanks. ...
written 9 weeks ago by rob234king560
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script for task or AWK
... I have tried to break a problem down to two files. I want to take the most common 2nd column value for each sequence (1st column) then have the range of column 3 for those values. Also count the number of markers so the number of Fc06 for seq000001. Any idea how to do this? I was hoping for somethin ...
script awk written 9 weeks ago by rob234king560 • updated 9 weeks ago by dariober9.3k
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falcon unzip output
... I have had errors getting falcon unzip to work on a pacbio assembly but believe I have got to an end by launching jobs manually. I had to change one of the scripts as -mum for nucmer was an option when should have been --mum and was causing an error (I did post on github about this). What I think ...
falcon pacbio written 3 months ago by rob234king560
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Comment: C: falcon-unzip installation and testing using pacbio data
... I got the test data to run using the config file provided in tutorial. It looks like was successful. The raw data was fasta. I just tested with fastq data and ends with error. From ENA they quite often provide the data in fastq so using this tools looks like I can convert https://github.com/zyndagj ...
written 5 months ago by rob234king560

Latest awards to rob234king

Popular Question 4 months ago, created a question with more than 1,000 views. For start codon gff annotation corrections using fasta file
Great Question 12 months ago, created a question with more than 5,000 views. For Indel Discovery Delly, Pindel, Samtools, Gatk
Popular Question 12 months ago, created a question with more than 1,000 views. For How to produce a hom/het snp frequency table
Popular Question 12 months ago, created a question with more than 1,000 views. For scripting problem to change string match of one file to another
Popular Question 12 months ago, created a question with more than 1,000 views. For Linux command line use to rename a gff annotation file "Name" attribute
Popular Question 12 months ago, created a question with more than 1,000 views. For Genemark-Es Gtf Output Conversion To Mod
Appreciated 18 months ago, created a post with more than 5 votes. For A: How To Remove Common Variants Present In Two Vcf Files?
Popular Question 18 months ago, created a question with more than 1,000 views. For Linux command line use to rename a gff annotation file "Name" attribute
Popular Question 18 months ago, created a question with more than 1,000 views. For Genemark-Es Gtf Output Conversion To Mod
Popular Question 18 months ago, created a question with more than 1,000 views. For Varscan.V2.3.6 False Positive Snps Being Called
Popular Question 18 months ago, created a question with more than 1,000 views. For scripting problem to use ProtComp output to identify secretome proteins
Great Question 2.0 years ago, created a question with more than 5,000 views. For New Free Community Tutorial Website For Bioinformatics Learning
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Merging Multiple De Novo Assembly Fasta Files
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: How To Remove Common Variants Present In Two Vcf Files?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Merging Multiple De Novo Assembly Fasta Files

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