User: hurfdurf

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hurfdurf460
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8 months, 2 weeks ago
Joined:
8 years, 10 months ago
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Posts by hurfdurf

<prev • 19 results • page 1 of 2 • next >
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Answer: A: Efficiently Iterating Over Fastq Records From Python
... Yet another option, but python 3.5+ only: https://github.com/lgautier/fastq-and-furious ...
written 10 months ago by hurfdurf460
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Answer: A: blastp commandline: against a protein database of a specific organism
... Another alternative is to download all the peptide sequences using BioMart for your genome of interest. Choose Ensembl Genes --> Homo Sapiens --> Sequences, then choose peptides, output to FASTA, and save.  Then build locally as you would any other blast database.  This will obviously miss he ...
written 4.5 years ago by hurfdurf460
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Answer: A: Comparing SNPs from different chips and genome versions as long as they have the
... Different genome versions will have different position offsets.  You could validate older genome versions by using a tool like LiftOver on the positions then seeing if the new coordinates agree with the latest genome dbSNP coordinates. Comparing across genome versions always introduces errors and e ...
written 4.7 years ago by hurfdurf460
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Answer: A: Circular Genome??
... Geneious has a circular-capable assembler built in now: http://blog.geneious.com/post/84370864944/building-a-circular-de-novo-assembler https://www.youtube.com/watch?v=rB6rYeVedfA ...
written 4.7 years ago by hurfdurf460
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Answer: A: Looking For Tools That Support Visual Comparisons Of Trace Files
... I don't think it will do subtraction, but SeqTrace may be worth a look. It will do forward and reverse read comparisons. Python and GPL'ed software. ...
written 6.4 years ago by hurfdurf460
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Answer: A: Regular Expression For Real World Gene Symbols?
... The full HGNC specs are here. Every source of gene names has different exception cases, and even the official HGNC names get cleaned up periodically, so a valid name can become invalid over time. If you are writing a validator for a known species just do a case insensitive lookup to an actual gene ...
written 6.4 years ago by hurfdurf460
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Comment: C: Drawing Chromosome Ideogams With Data
... Just a quick note, quantsmooth seems to use ISCN coordinates (with human, at least) so if you are using UCSC or EnsEMBL coordinates you may have to remap to avoid telomeric overruns. ...
written 7.1 years ago by hurfdurf460
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What Are Some Good Resources To Convince Biologists To Power Studies Appropriately?
... I've been given an opportunity to produce some guidelines for design of microarray experiments. I know there many resources and guides for determining approprate microarray experiment sample sizes. However, what I'm looking for are data sets or examples that will actually convince non-math friend ...
microarray affymetrix written 7.3 years ago by hurfdurf460 • updated 7.3 years ago by Mary11k
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Comment: C: Fedora Or Red Hat?
... What type of work do you anticipate doing on this system? Is it a desktop or a server? Are you going to be installing older existing packages, compiling bleeding edge software, and/or developing new software? ...
written 8.4 years ago by hurfdurf460
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Answer: A: How Are Gene Synonyms Defined
... The canonical gene identifiers (as defined by HUGO, Refseq, Ensembl, etc.) have to be unique. Synonym lists are used to aid in looking at legacy publications which use old imprecise names. In the case of SCG2, it's probable that MEN1 was somehow conflated with SCG2 in the literature, so some of th ...
written 8.4 years ago by hurfdurf460

Latest awards to hurfdurf

Popular Question 4.5 years ago, created a question with more than 1,000 views. For What Are Some Good Resources To Convince Biologists To Power Studies Appropriately?
Popular Question 4.5 years ago, created a question with more than 1,000 views. For What Is The Best And Most Complete Source Of Secretory Data For Mammalian Genes?
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: Test Whether The Variance In A Group Is Lower Than In Another
Student 7.3 years ago, asked a question with at least 3 up-votes. For What Are Some Good Resources To Convince Biologists To Power Studies Appropriately?
Good Question 7.3 years ago, asked a question that was upvoted at least 5 times. For What Are Some Good Resources To Convince Biologists To Power Studies Appropriately?
Popular Question 8.5 years ago, created a question with more than 1,000 views. For Pymol - Independent Rotation Axes For Multiple Molecules
Teacher 8.7 years ago, created an answer with at least 3 up-votes. For A: Test Whether The Variance In A Group Is Lower Than In Another
Appreciated 8.7 years ago, created a post with more than 5 votes. For A: Annotation For Affymetrix Probe Id "241838_At"
Good Answer 8.7 years ago, created an answer that was upvoted at least 5 times. For A: Annotation For Affymetrix Probe Id "241838_At"
Teacher 8.7 years ago, created an answer with at least 3 up-votes. For A: Annotation For Affymetrix Probe Id "241838_At"
Teacher 8.8 years ago, created an answer with at least 3 up-votes. For A: Determine Whether A Gene Product Is A Transcription Factor
Student 8.8 years ago, asked a question with at least 3 up-votes. For What Is The Best And Most Complete Source Of Secretory Data For Mammalian Genes?
Good Question 8.8 years ago, asked a question that was upvoted at least 5 times. For What Is The Best And Most Complete Source Of Secretory Data For Mammalian Genes?

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