User: joshualevipayne

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70
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Zurich
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https://sites.google.c...
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Last seen:
4 months, 1 week ago
Joined:
7 years, 2 months ago
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Posts by joshualevipayne

<prev • 11 results • page 1 of 2 • next >
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Answer: A: Differences between FPKM and FPKM-UQ files in gene expression analysis
... This link might also be helpful: https://gdc-docs.nci.nih.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/ ...
written 3.6 years ago by joshualevipayne70
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Answer: A: Ideas or advise for data visualization that shows genotype and phenotpye relatio
... You may also be able to use the "genotype network" formalism, creating a separate network for each phenotype. In a genotype network, a vertex represents a sequence and edges connect vertices if their corresponding sequences are separated by a single, small mutation. For more information on this form ...
written 6.1 years ago by joshualevipayne70
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Comment: C: Where To Find Encode Dnase I Footprint Data
... Direct from the source! Thank you sjneph, much appreciated. ...
written 6.3 years ago by joshualevipayne70
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Comment: C: Where To Find Encode Dnase I Footprint Data
... Thanks Mikael, but the link you provided is just a mirror of the link I posted. It's unclear what the narrowPeak files contain. One would think they would contain the data summarized in the "Hotspot Regions (FDR 1%)" column of Table S1 in Neph et al. (2012). However, the K562 narrowPeak file contai ...
written 6.3 years ago by joshualevipayne70
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Where To Find Encode Dnase I Footprint Data
... Hello. I would like to download the ENCODE DNase I footprint data for the 41 human cell and tissue types described by Neph et al. (2012) Nature, 489:83-90. Here is an example to illustrate my question. Consider only a single human cell type, K562. The following DNase I data files can be found via ...
encode written 6.3 years ago by joshualevipayne70 • updated 6.3 years ago by sjneph620
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Comment: C: Extracting Random Sequences From A Large Fasta File Using Bioperl
... Hi Pierre, Sorry if this thread appears redundant, but I don't think that it actually is; neither of the linked threads discuss Bio::DB::Fasta. In these linked threads, you provide a solution that requires shuff. This isn't a favorable solution here due to the large file size. Chris Penkett's solu ...
written 6.3 years ago by joshualevipayne70
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Extracting Random Sequences From A Large Fasta File Using Bioperl
... Hello. I have a large fasta file, approximately 4.5GB (hg19, est.fa). I would like to extract a number of sequences from this file at random and without replacement. I've followed some wonderful advice in an earlier thread (Extracting multiple fasta sequences at a time from a file containing MANY ...
fasta bioperl written 6.3 years ago by joshualevipayne70 • updated 6.2 years ago by Alex Reynolds30k
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Comment: C: Looking For Fasta Files Of Intergenic Regions For Mouse (Mm9) And Worm (Ce10)
... Thanks Neal, this is a good solution. Bedtools is amazingly useful. For mus, I've decided to use the 1000 bp segments upstream of all annotated transcription start sites, which can be downloaded directly here: http://hgdownload-test.cse.ucsc.edu/goldenPath/mm9/bigZips/ ...
written 7.0 years ago by joshualevipayne70
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Looking For Fasta Files Of Intergenic Regions For Mouse (Mm9) And Worm (Ce10)
... I'm looking for a fasta file of all intergenic regions for mouse (mm9) and worm (ce10). Ideally, I want to find the equivalent of the NotFeature.fasta file for yeast (S288c), which can be found here: http://downloads.yeastgenome.org/sequence/S288C_reference/intergenic/ This file "contains DNA sequ ...
written 7.0 years ago by joshualevipayne70 • updated 7.0 years ago by neal.platt220
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Answer: A: Problem Fetching Sequences From A Bed File With Galaxy
... Thanks seninp, that's it. The chromosomes should be specified with Roman numerals. All set now. ...
written 7.2 years ago by joshualevipayne70

Latest awards to joshualevipayne

Great Question 2.5 years ago, created a question with more than 5,000 views. For Extracting Random Sequences From A Large Fasta File Using Bioperl
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Differences between FPKM and FPKM-UQ files in gene expression analysis
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Looking For Fasta Files Of Intergenic Regions For Mouse (Mm9) And Worm (Ce10)
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Problem Fetching Sequences From A Bed File With Galaxy
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Where To Find Encode Dnase I Footprint Data
Student 5.0 years ago, asked a question with at least 3 up-votes. For Where To Find Encode Dnase I Footprint Data
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Extracting Random Sequences From A Large Fasta File Using Bioperl

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