User: Daniel
Daniel • 3.7k
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Posts by Daniel
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... 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
Daniel • 3.7k
1
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4
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496
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4
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... Or Just Another Bogus Bioinformatics Algorithm!
http://www.acgt.me/blog?tag=jabba ...
written 3 months ago by
Daniel • 3.7k
0
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0
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140
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0
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... 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
Daniel • 3.7k
1
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0
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140
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... 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 ...
written 5 months ago by
Daniel • 3.7k
1
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3
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390
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3
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... 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
Daniel • 3.7k
0
votes
3
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390
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3
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... 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
Daniel • 3.7k
4
votes
3
answers
390
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3
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... 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
Daniel • 3.7k
0
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0
answers
410
views
0
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... 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( ...
written 9 months ago by
Daniel • 3.7k
0
votes
2
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508
views
2
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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
Daniel • 3.7k
2
votes
2
answers
3.2k
views
2
answers
... 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
Daniel • 3.7k
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