User: Daniel
Daniel • 3.8k
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- Location:
- Cardiff University
- Last seen:
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- Joined:
- 9 years, 9 months ago
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Posts by Daniel
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... This is an interesting requirement: "*A Ph.D. earned no earlier than 2015 is required*".
What is the rationale behind that? ...
written 20 months ago by
Daniel • 3.8k
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755
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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 22 months ago by
Daniel • 3.8k
1
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4
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850
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4
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... Or Just Another Bogus Bioinformatics Algorithm!
http://www.acgt.me/blog?tag=jabba ...
written 2.1 years ago by
Daniel • 3.8k
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488
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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 2.2 years ago by
Daniel • 3.8k
1
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488
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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 2.2 years ago by
Daniel • 3.8k
1
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3
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968
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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 2.5 years ago by
Daniel • 3.8k
0
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3
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968
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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 2.5 years ago by
Daniel • 3.8k
4
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3
answers
968
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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 2.5 years ago by
Daniel • 3.8k
1
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0
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1.7k
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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 2.6 years ago by
Daniel • 3.8k
• updated
11 weeks ago by
wangdepin5135 • 0
0
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2
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1.1k
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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 3.0 years ago by
Daniel • 3.8k
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For RNAseq comparisons (tophat->HTSeq->edgeR) return only a few sig diffs, and all snRNA. Pos. bias? Further options?
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For RNAseq comparisons (tophat->HTSeq->edgeR) return only a few sig diffs, and all snRNA. Pos. bias? Further options?
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For A: Correcting sequence reads based on ORF disruption from reference sequence.
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For A: Convert Fas/Qual Into Fastq?
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For RNAseq comparisons (tophat->HTSeq->edgeR) return only a few sig diffs, and all snRNA. Pos. bias? Further options?
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For A: Correcting sequence reads based on ORF disruption from reference sequence.
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For RNAseq comparisons (tophat->HTSeq->edgeR) return only a few sig diffs, and all snRNA. Pos. bias? Further options?
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For RNAseq comparisons (tophat->HTSeq->edgeR) return only a few sig diffs, and all snRNA. Pos. bias? Further options?
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2.3 years ago,
created a question with more than 1,000 views.
For RNAseq comparisons (tophat->HTSeq->edgeR) return only a few sig diffs, and all snRNA. Pos. bias? Further options?
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For RNAseq comparisons (tophat->HTSeq->edgeR) return only a few sig diffs, and all snRNA. Pos. bias? Further options?
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2.4 years ago,
created an answer that has been accepted.
For A: Correcting sequence reads based on ORF disruption from reference sequence.
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For Determining Transcription Start Sites from multiple RNAseq bioreps
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For Determining Transcription Start Sites from multiple RNAseq bioreps
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2.5 years ago,
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For Parsing Genbank Format In Bioperl.
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For A: Convert Fas/Qual Into Fastq?
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For Is there a more optimal SAM orientation parsing method?
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2.6 years ago,
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For Determining Transcription Start Sites from multiple RNAseq bioreps
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2.7 years ago,
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For Determining Transcription Start Sites from multiple RNAseq bioreps
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2.7 years ago,
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For Parsing Genbank Format In Bioperl.
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