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User: Daniel

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Daniel • 3.3k
Reputation:
3,310
Status:
Trusted
Location:
Cardiff University
Last seen:
20 hours ago
Joined:
6 years, 4 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 8 weeks ago by Daniel • 3.3k
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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 10 weeks ago by Daniel • 3.3k
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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 10 weeks ago by Daniel • 3.3k
6
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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 10 weeks ago by Daniel • 3.3k
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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 10 weeks ago by Daniel • 3.3k
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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 10 weeks ago by Daniel • 3.3k
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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 11 weeks ago by Daniel • 3.3k
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Comment: C: fasta seq header
... Simpler: `sed -i 's/|.*//' gene.fasta` ...
written 11 weeks ago by Daniel • 3.3k
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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 12 weeks ago by Daniel • 3.3k
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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 3 months ago by Daniel • 3.3k

Latest awards to Daniel

Appreciated 20 days ago, created a post with more than 5 votes. For A: Conferences On Bioinformatics
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Travel and accommodation bursaries for workshops on Gene expression analysis, Metabolomics, RAD analysis or Population genomics in Environmental ‘Omics
Scholar 12 weeks ago, created an answer that has been accepted. For A: Correcting sequence reads based on ORF disruption from reference sequence.
Student 4 months 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?
Popular Question 4 months ago, created a question with more than 1,000 views. For Travel and accommodation bursaries for workshops on Gene expression analysis, Metabolomics, RAD analysis or Population genomics in Environmental ‘Omics
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Convert Fas/Qual Into Fastq?
Good Question 7 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 7 months ago, created a comment with at least 3 up-votes. For C: Why Didn'T Biostar Join Stack Exchange?
Popular Question 8 months ago, created a question with more than 1,000 views. For Error when fuzzy sequence matching using String::Approx in perl
Popular Question 8 months ago, created a question with more than 1,000 views. For WORKSHOP: Computational Approaches to Study Biological Mechanisms. Bringing together large scale ‘omics approaches and classical computational modelling. REGISTRATION FEES NOW COVERED
Appreciated 9 months ago, created a post with more than 5 votes. For A: Conferences On Bioinformatics
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Why Didn'T Biostar Join Stack Exchange?
Popular Question 12 months ago, created a question with more than 1,000 views. For Travel and accommodation bursaries for workshops on Gene expression analysis, Metabolomics, RAD analysis or Population genomics in Environmental ‘Omics
Popular Question 12 months ago, created a question with more than 1,000 views. For Travel and accommodation bursaries for workshops on Gene expression analysis, Metabolomics, RAD analysis or Population genomics in Environmental ‘Omics
Popular Question 12 months ago, created a question with more than 1,000 views. For Travel and accommodation bursaries for workshops on Gene expression analysis, Metabolomics, RAD analysis or Population genomics in Environmental ‘Omics
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
Scholar 13 months ago, created an answer that has been accepted. For A: Correcting sequence reads based on ORF disruption from reference sequence.
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Convert Fas/Qual Into Fastq?
Scholar 13 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 13 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 14 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 14 months ago, created an answer with at least 3 up-votes. For A: Convert Fas/Qual Into Fastq?
Appreciated 14 months ago, created a post with more than 5 votes. For A: Conferences On Bioinformatics
Great Question 15 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?
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