User: secretjess

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secretjess170
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Cambridge
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2 years, 10 months ago
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4 years, 5 months ago
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Posts by secretjess

<prev • 27 results • page 1 of 3 • next >
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Comment: C: Easy matching of a transcription factor binding motif to a DNA promoter sequence
... Great! Thank you - I was trying to use FIMO but I didn't know how to generate a motif file. Your answer is really helpful, thanks a lot (P.S. I cannot upvote or accept this answer for some reason) ...
written 2.9 years ago by secretjess170
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Easy matching of a transcription factor binding motif to a DNA promoter sequence
... I've been gathering some evidence that several genes are directly regulated by a particular transcription factor I find interesting. I've obtained the transcription factor's binding motif from literature/PAZAR and downloaded sequences 1000 bases to the 5' end of my putative target genes. Obviously ...
transcription factor meme promoter motif match written 2.9 years ago by secretjess170 • updated 2.9 years ago by PyPerl760
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Answer: A: Amino Acid Composition-Graphic Representation
... In R: rand_seq <- "WYEGYQERKMKKNLLGYEQMLRSDFMNTMHPHEDTWICWDYALNQIALNPKTWKVQKSCKASLMPTVDSMYFWYIAHMEMKMQYEWTEWFIHVPYFFDRCFVWYDEFCCQVCMAFLERFRDTNQSSGQLCAWVGYLKNIGYSHYISTILYRYPQEYNIVPTWNIAIMHMQDKVDVECKLNKSMSEHCHHHFPLLAYIDFPLWKPNIYKSPWLMDPFMANLA" aa_tab <- table(strsplit(rand_seq,"")) pie(aa_tab ...
written 3.7 years ago by secretjess170
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Comment: C: 1000G Query / Using Tabix With A Proxy
... Using either of those commands shows 0.2.6 but if I just tabix to start up the program (it displays help) then it says Version: 0.2.5 (r1005) ...
written 3.7 years ago by secretjess170
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Comment: C: 1000G Query / Using Tabix With A Proxy
... Downloaded the newest (0.2.6) tabix and installed it by following http://genometoolbox.blogspot.co.uk/2013/11/installing-tabix-on-unix.html. The folder is called tabix-0.2.6 but when I run tabix it claims it's "Version: 0.2.5". Bit strange, but either way - thanks for the help but I still can't get ...
written 3.7 years ago by secretjess170
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Comment: C: 1000G Query / Using Tabix With A Proxy
... Thanks both! That makes sense. I should probably update the release I'm looking at too. I intended this question to resolve my issues with using tabix behind a proxy, but I hadn't considered that the download might break. ...
written 3.7 years ago by secretjess170
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1000G Query / Using Tabix With A Proxy
... When I run the following command the connection times out: ./tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz 1:57000000-57001000 > test.vcf connect: Connection timed out [main] fail to open the data file But if I run this it wor ...
tabix vcftools written 3.7 years ago by secretjess170 • updated 3.1 years ago by Biostar ♦♦ 20
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Gpr File - Dual Or Single Colour?
... I have several .gpr files (and the corresponding .gal file) but I have no further information available to me. I've never done this before but I am trying to follow online tutorials (http://www.bioconductor.org/packages/2.12/bioc/vignettes/limma/inst/doc/usersguide.pdf and http://www.computing.dcu.i ...
R limma written 4.0 years ago by secretjess170 • updated 4.0 years ago by Michael Dondrup42k
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Comment: C: Compare 2 Affymetrix Probesets
... I eventually managed it using two Ensembl Biomart queries but thanks, that looks like it would work too :) ...
written 4.3 years ago by secretjess170
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Compare 2 Affymetrix Probesets
... I'd like to see what genes are detected using a Human Genome U133 Plus 2.0 Array that aren't in a Human Genome U133A 2.0 Array. I'm slowly slowly working my way through the files available on http://www.affymetrix.com/browse/products.jsp?productId=131455 http://www.affymetrix.com/estore/browse/pr ...
affymetrix probeset written 4.3 years ago by secretjess170 • updated 4.3 years ago by AndreiR240

Latest awards to secretjess

Popular Question 3.7 years ago, created a question with more than 1,000 views. For Reindex A Vcf File / How To Handle Cosmic Vcf Files
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Retrieve All Genes Contained Within A Specific Chromosomal Region Using R And Biomart
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Amino Acid Composition-Graphic Representation
Student 4.4 years ago, asked a question with at least 3 up-votes. For 200Bp Long Query Returning 201Bp
Student 4.4 years ago, asked a question with at least 3 up-votes. For Retrieve All Genes Contained Within A Specific Chromosomal Region Using R And Biomart

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