User: Daniel

gravatar for Daniel
Daniel3.3k
Reputation:
3,290
Status:
Trusted
Location:
Cardiff University
Last seen:
3 hours ago
Joined:
6 years, 2 months ago
Email:
d*****************@googlemail.com

Posts by Daniel

<prev • 353 results • page 1 of 36 • next >
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Comment: C: else condition in awk
... If it's not working don't click 'accept' and tell us what the error is. ...
written 5 days ago by Daniel3.3k
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132
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Comment: C: How many lanes does the Nextseq (illumina) flow cell have?
... This is misleading, because although the NextSeq has 4 lanes, they aren't physically isolated and only one pooled library can be used, unlike the physical separation in the HiSeq. I think this is normally what people are looking for when asking about number of lanes. ...
written 19 days ago by Daniel3.3k
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126
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Comment: C: What is the limiting factor for trimmomatic speed and how can it be increased?
... Fantastic, I'll give this a go! ...
written 19 days ago by Daniel3.3k
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2
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7 follow
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What is the limiting factor for trimmomatic speed and how can it be increased?
... I'm using trimmomatic mainly to filter out adapters in the read through of my paired end illumina data. My command is as follows, and produces expected results: java -jar trimmomatic-0.33.jar PE 01_R1.fastq 01_R2.fastq 01_R1-trimpair.fastq 01_R1-trimunpair.fastq 01_R2-trimpair.fastq 01_R2-trim ...
trimmomatic fastq written 20 days ago by Daniel3.3k
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Answer: A: Progress bar to measure blast running time?
... I too am impatient and want to monitor how my runs are going. While what people are saying above is correct that there's not a built in method, what I normally do is use `watch` with either `grep -c ` or `wc -l` depending on your output format. But if you want to do it in your script, either read i ...
written 21 days ago by Daniel3.3k
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Comment: C: Senior Bioinformatician (Jones Group, Hinxton, Cambridge UK)
... Where do you apply to? There's no link here and the post isn't up on http://www.jobs.ac.uk/employer/wellcome-trust-sanger-institute ...
written 21 days ago by Daniel3.3k
0
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8
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8
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Comment: C: fasta seq header
... That's fair, yeah. Don't use `-i` until you're sure it's doing what you think it's doing! ...
written 29 days ago by Daniel3.3k
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Comment: C: fasta seq header
... Simpler: `sed -i 's/|.*//' gene.fasta` ...
written 29 days ago by Daniel3.3k
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Answer: A: Fasta file edition
... The first ever perl script I wrote does this! Adds a different barcode based on a common fasta header identifier, which I think that's what you want? All you do is `add_barcode.pl my_file.fasta` then it'll ask you for the shared ID in the header, then ask for what the barcode you want to add is. No ...
written 4 weeks ago by Daniel3.3k
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Answer: A: analysing retrieved RNAseq datasets from GEO
... I recommend working through the **RNA-seqlopedia** website before going any further, to understand what is possible and what is typical in an RNAseq analysis: http://rnaseq.uoregon.edu ...
written 6 weeks ago by Daniel3.3k

Latest awards to Daniel

Scholar 4 weeks ago, created an answer that has been accepted. For A: Correcting sequence reads based on ORF disruption from reference sequence.
Student 10 weeks ago, asked a question with at least 3 up-votes. For Rdp, Greengenes And Arb-Silva. Are There Any Advantages Of One Over The Other?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Convert Fas/Qual Into Fastq?
Good Question 5 months ago, asked a question that was upvoted at least 5 times. For Rdp, Greengenes And Arb-Silva. Are There Any Advantages Of One Over The Other?
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Why Didn'T Biostar Join Stack Exchange?
Popular Question 6 months ago, created a question with more than 1,000 views. For Error when fuzzy sequence matching using String::Approx in perl
Appreciated 7 months ago, created a post with more than 5 votes. For A: Conferences On Bioinformatics
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Why Didn'T Biostar Join Stack Exchange?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Convert Fas/Qual Into Fastq?
Appreciated 11 months ago, created a post with more than 5 votes. For A: Conferences On Bioinformatics
Scholar 11 months ago, created an answer that has been accepted. For A: Correcting sequence reads based on ORF disruption from reference sequence.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Convert Fas/Qual Into Fastq?
Scholar 11 months ago, created an answer that has been accepted. For A: Is there a succinct method of isolating sequences phylogenetically similar to a
Good Question 11 months ago, asked a question that was upvoted at least 5 times. For Rdp, Greengenes And Arb-Silva. Are There Any Advantages Of One Over The Other?
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: Should We Accept The Terms For The Migration To Stackexchange 2.0
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Convert Fas/Qual Into Fastq?
Appreciated 12 months ago, created a post with more than 5 votes. For A: Conferences On Bioinformatics
Great Question 13 months ago, created a question with more than 5,000 views. For Rdp, Greengenes And Arb-Silva. Are There Any Advantages Of One Over The Other?
Popular Question 17 months ago, created a question with more than 1,000 views. For Is There A Library Of Fosmid Sequences?

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