User: Daniel

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Daniel3.7k
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Cardiff University
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Posts by Daniel

<prev • 365 results • page 1 of 37 • next >
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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 5 weeks 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 3 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 5 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 5 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 8 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 8 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 8 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 9 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 15 months ago by Daniel3.7k
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Answer: A: FASTA file into excel file format?
... There are lots of jokes above, but the honest answer is that you do not want to do this. Once you have converted the file it would be so massive that it would impossible to open and use in excel before any other problems. Further, this is not an appropriate way to read the data, and 99.9% of the tim ...
written 16 months ago by Daniel3.7k

Latest awards to Daniel

Epic Question 4 weeks 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 5 months ago, created a question with more than 5,000 views. For Subsample BAM to fixed number of alignments
Scholar 8 months ago, created an answer that has been accepted. For A: Correcting sequence reads based on ORF disruption from reference sequence.
Popular Question 8 months ago, created a question with more than 1,000 views. For Determining Transcription Start Sites from multiple RNAseq bioreps
Popular Question 8 months ago, created a question with more than 1,000 views. For Determining Transcription Start Sites from multiple RNAseq bioreps
Great Question 8 months ago, created a question with more than 5,000 views. For Parsing Genbank Format In Bioperl.
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Convert Fas/Qual Into Fastq?
Popular Question 9 months ago, created a question with more than 1,000 views. For Determining Transcription Start Sites from multiple RNAseq bioreps
Popular Question 9 months ago, created a question with more than 1,000 views. For Is there a more optimal SAM orientation parsing method?
Popular Question 11 months ago, created a question with more than 1,000 views. For Determining Transcription Start Sites from multiple RNAseq bioreps
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Convert Fas/Qual Into Fastq?
Great Question 11 months ago, created a question with more than 5,000 views. For Parsing Genbank Format In Bioperl.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Conferences On Bioinformatics
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: Why Didn'T Biostar Join Stack Exchange?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Convert Fas/Qual Into Fastq?

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