User: Daniel

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Daniel3.7k
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Location:
Cardiff University
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8 years, 6 months ago
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Posts by Daniel

<prev • 366 results • page 1 of 37 • next >
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Comment: C: Research Associate in Genomics / Statistical Genetics (USA)
... This is an interesting requirement: "*A Ph.D. earned no earlier than 2015 is required*". What is the rationale behind that? ...
written 5 months ago by Daniel3.7k
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Answer: A: Bioinformatic tools for MyCOBIOME analysis.
... There are ITS databases that are used with qiime2 and several tutorials and pipelines that people have written up: https://github.com/gregcaporaso/2017.06.23-q2-fungal-tutorial https://forum.qiime2.org/t/its-data-in-qiime2/4087 As long as you're using the correct database it should all be fine to ...
written 7 months ago by Daniel3.7k
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Comment: C: Bioinformatics terms that might be confusing for beginners
... Or Just Another Bogus Bioinformatics Algorithm! http://www.acgt.me/blog?tag=jabba ...
written 10 months ago by Daniel3.7k
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Comment: C: Statistically defining deep branching clades in phylogenetic tree
... Thanks for the suggestion. I've been giving it a go but it's basically only identifying everything into one cluster. Having a look at ete but not solved it yet. ...
written 11 months ago by Daniel3.7k
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Statistically defining deep branching clades in phylogenetic tree
... I have a phylogenetic tree which visually has 3 major clades, one of which forks into two minor clades. I am discussing the groups in the text in regards to the metadata but I want to statistically/technically describe why the groups are seperate. What is the best way to achieve this? The tree is U ...
phylogenetics trees written 11 months ago by Daniel3.7k
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Comment: C: fasta to bed format with more information that just chr locations
... The $n parameters are the columns when you divide the file up by what is inside the -F'[ ]' box, so if you split the line every time you saw a space, asterix, colon, or period then you'd want the 5th, 6th, 8th and 13th columns to be printed. ...
written 14 months ago by Daniel3.7k
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Comment: C: fasta to bed format with more information that just chr locations
... Huh, I was certain that bed format was colon and hyphen but the internet doesn't support that... Maybe I'm going mad. Ok, updating. Edit: I was thinking of UCSC browser formatting apparently. ...
written 14 months ago by Daniel3.7k
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Answer: A: fasta to bed format with more information that just chr locations
... My approach is lazier... Just split on the punctuation, pull out the columns you want, and separate by "\t". awk -F'[ *:.]' -v OFS="\t" '{print "chr"$5,$6,$8,$13}' tmp.txt # Output chr2L 22300300 22304444 invader2 ...
written 14 months ago by Daniel3.7k
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Tutorial: How to get full taxonomy classification using taxize and myTAI
... There are lots of questions regarding this, and I have asked them myself over the years, but I've recently found this tool which is great and I thought I'd put a standard example. This might not be the best way of parsing the outputs in R, but as a tool it generates all the right data! library( ...
R tutorial taxonomy tool written 15 months ago by Daniel3.7k
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Comment: C: convert illumina to fastq Sanger
... Please explain what you are trying to achieve and why, so that we can help you, as this request is confusing. Do you have a bcl file? ...
written 21 months ago by Daniel3.7k

Latest awards to Daniel

Great Question 5 months ago, created a question with more than 5,000 views. For Subsample BAM to fixed number of alignments
Epic Question 7 months ago, created a question with more than 10,000 views. For Rdp, Greengenes And Arb-Silva. Are There Any Advantages Of One Over The Other?
Great Question 11 months ago, created a question with more than 5,000 views. For Subsample BAM to fixed number of alignments
Scholar 14 months ago, created an answer that has been accepted. For A: Correcting sequence reads based on ORF disruption from reference sequence.
Popular Question 14 months ago, created a question with more than 1,000 views. For Determining Transcription Start Sites from multiple RNAseq bioreps
Popular Question 14 months ago, created a question with more than 1,000 views. For Determining Transcription Start Sites from multiple RNAseq bioreps
Great Question 14 months ago, created a question with more than 5,000 views. For Parsing Genbank Format In Bioperl.
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Convert Fas/Qual Into Fastq?
Popular Question 15 months ago, created a question with more than 1,000 views. For Is there a more optimal SAM orientation parsing method?
Popular Question 15 months ago, created a question with more than 1,000 views. For Determining Transcription Start Sites from multiple RNAseq bioreps
Great Question 17 months ago, created a question with more than 5,000 views. For Parsing Genbank Format In Bioperl.
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Conferences On Bioinformatics
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Convert Fas/Qual Into Fastq?
Popular Question 17 months ago, created a question with more than 1,000 views. For Determining Transcription Start Sites from multiple RNAseq bioreps
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: Why Didn'T Biostar Join Stack Exchange?

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