User: c.v.oflynn

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c.v.oflynn90
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Posts by c.v.oflynn

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Job: Bioinformatics Scientist - Waltham Center for Pet Nutrition, East Midlands, UK
... Talented bioinformatician (junior/senior) looking for a job in industry? Love 🐶,🐱,🐠? The [WALTHAM][1] Centre for Pet Nutrition has been advancing research into the nutrition and health of pets for over 50 years and is the fundamental science centre for [Mars Petcare][2]. We focus on the nutrition ...
microbiome cat job genomics dog written 2.0 years ago by c.v.oflynn90 • updated 2.0 years ago by genomax73k
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Answer: A: vcftools: the length of each row is not same
... Hi zwang10, did you solve this? the first column of chr1.012 is numeric sample id, not genotype. remove this and you have the same lengths. Ciaran ...
written 2.8 years ago by c.v.oflynn90
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Comment: C: Automating Flash Sequence Joins
... ls *_1.fastq | grep -Poh ".*_1" | sed 's/1$//' will work if the number of underscores is not always the same ...
written 3.5 years ago by c.v.oflynn90
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Answer: A: Automating Flash Sequence Joins
... A for loop would do the trick, assuming the paired reads are named like; reads1_1.fq reads1_2.fq for i in $(ls *fq | grep "_1" | cut -f 1 -d "_"); do flash ${i}_1.fq ${i}_2.fq; done ...
written 3.5 years ago by c.v.oflynn90
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Aligning high depth data to short target sequence
... Hi All,  Just a general query regarding best practice;  What is the BEST way to align WGS data to an individual gene or fragment?  Example: I have several libraries of high coverage shotgun sequence from my favourite organism. I have previously aligned this data to the latest high quality draft g ...
whole genome alignment resequencing target written 3.7 years ago by c.v.oflynn90 • updated 3.7 years ago by Devon Ryan92k
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Answer: A: How can I save a pvclust object?
... could you use save.image() ? and then use load() on the saved file.  ...
written 4.6 years ago by c.v.oflynn90
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Comment: C: convert legacy blast parameters to blastn
... Thanks Siva, helped a lot ...
written 4.8 years ago by c.v.oflynn90
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How to plot UniFrac PCoA with 95% confidence Elipses in R
... Hi Guys,  I'm having difficulty plotting a PCoA for UniFrac distances with elipses. I'm using phyloseq to compute an ordination object and then creating elipses with ordiellipse() from vegan package. I can do almost exactly what I want for correspondence analysis (CCA), as in example below, or prin ...
vegan R metagenomics phyloseq ordiellipse written 4.8 years ago by c.v.oflynn90 • updated 4.6 years ago by Biostar ♦♦ 20
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convert legacy blast parameters to blastn
... Hi all, I am following the parameters given in a paper for performing blast. The parameters given are in the old format;  -X 150 -q -1 -F F Could anyone convert them to the current blastn format? eg (throws errors); -xdrop_gap_final 150 -penalty -1 -dust no I could use the old blast, but i ...
parameters blast written 4.9 years ago by c.v.oflynn90 • updated 4.9 years ago by Siva1.6k
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Answer: A: Are There Any Databases/Knowledge Bases Or Other Resources Concerning Bacterial
... Interesting question, this was the best that I have found. http://ardb.cbcb.umd.edu/. It is not huge and not maintained since 2009. ...
written 5.7 years ago by c.v.oflynn90

Latest awards to c.v.oflynn

Popular Question 3.4 years ago, created a question with more than 1,000 views. For Bulk Rast To Ncbi/Ebi/Genbank
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Automating Flash Sequence Joins
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Ncbi Tax Id For Draft Bacteria Genomes
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Ncbi Tax Id For Draft Bacteria Genomes
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Ncbi Tax Id For Draft Bacteria Genomes

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