User: polarise

gravatar for polarise
polarise370
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370
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Location:
Galway, Ireland
Website:
http://www.paulkorir.com
Last seen:
2 years, 6 months ago
Joined:
6 years ago
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Posts by polarise

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Comment: C: What'S The Difference Between Cds And Orf?
... There is a lot of evidence of non-canonical translation that begins at non-AUG sense codons. For example, translation may begin at CUG, GUG or ACG (see http://www.sciencedirect.com/science/article/pii/0378111990900856). It is therefore more meaningful to define ORFs as stop to stop (rather than star ...
written 2.5 years ago by polarise370
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Comment: C: Ensembl chromosome name?
...     awk 'BEGIN{OFS="\t"}{print $1,"chr"$2,$3,$4,$5,$6}' genes.fpkm_tracking > genes_chr.fpkm_tracking where `genes_chr.fpkm_tracking` is the new file with 'chr' ...
written 2.9 years ago by polarise370
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Comment: C: How to generate .sra files from Fastq
... Out of curiosity: what would you like to do with *.sra files when you already have the *.bam/*.sam/*.fastq files? ...
written 3.4 years ago by polarise370
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Answer: A: Help with finding whole list of known snps
... The list of known SNPs for any organism will always be a work in progress because there are outstanding regions of the genome that remain to sequenced due to their complex nature (among other regions). Therefore, it makes more sense to start with what is available and keep the door open to re-runnin ...
written 3.4 years ago by polarise370
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Answer: A: Raw Data From Solid Sequencing
... Even though the data is available as Illumina NGS I think the SRA Toolkit can allow you to convert to SOLID colourspace format. The command to use is     abi-dump with more details at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc Best, P ...
written 3.4 years ago by polarise370
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Comment: C: R And Sqlite Db Locked Error
... I'm using the following package: http://bioconductor.org/packages/release/data/annotation/html/hugene10stprobeset.db.html The current solution is to install the package on the master node (if accessible) since that will have its own disk hence no NFS lock. ...
written 4.2 years ago by polarise370
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Comment: C: R And Sqlite Db Locked Error
... Perhaps if I stated that I was running a Bioconductor package it might draw it in... ;-) ...
written 4.2 years ago by polarise370
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R And Sqlite Db Locked Error
... I've become bald pulling out my hair because of this problem. Time and time again I need to run an R package that needs to use RSQLite but fails because of NFS locking. Well, that's the setup on our cluster. Curiously, I don't see other people complaining about this problem but I know that a lot of ...
R written 4.2 years ago by polarise370 • updated 4.2 years ago by Michael Dondrup43k
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Comment: C: A Bioinformatics Overview: What -Omics Approaches Exist?
... There's also metagenomics: see http://en.wikipedia.org/wiki/Metagenomics. ...
written 4.4 years ago by polarise370
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Comment: C: Normalization Of Gene Expression Using Rnaseq Rpkm Values
... The ranges of RPKM are 0 to 1e-6... That seems like a very narrow range. Did you mean 0 to 1e6 instead? ...
written 4.4 years ago by polarise370

Latest awards to polarise

Popular Question 3.6 years ago, created a question with more than 1,000 views. For Cost Comparison Between Microarray And Rna-Seq Experiment
Appreciated 4.0 years ago, created a post with more than 5 votes. For Expected Correlation Between Exon Array And Rna-Seq
Good Question 4.0 years ago, asked a question that was upvoted at least 5 times. For Expected Correlation Between Exon Array And Rna-Seq
Good Answer 4.0 years ago, created an answer that was upvoted at least 5 times. For A: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Cost Comparison Between Microarray And Rna-Seq Experiment
Supporter 4.0 years ago, voted at least 25 times.
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Calculate Exon Inclusion From Bed Files
Student 4.0 years ago, asked a question with at least 3 up-votes. For Expected Correlation Between Exon Array And Rna-Seq

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