User: joshualevipayne

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Posts by joshualevipayne

<prev • 12 results • page 1 of 2 • next >
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Example Python code for ViennaRNA
... Hi Biostars, I'm trying to work with the Python distribution of ViennaRNA. I've found almost no documentation, except for a few examples posted here: https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/helloworld_swig.html#helloworld_python I can replicate these, but I'm lost trying to use functi ...
viennarna rna folding python written 11 days ago by joshualevipayne70
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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 4.0 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 6.4 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 6.6 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 6.6 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 6.6 years ago by joshualevipayne70 • updated 6.6 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 6.6 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 6.6 years ago by joshualevipayne70 • updated 6.5 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 7.4 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 7.4 years ago by joshualevipayne70 • updated 7.4 years ago by neal.platt220

Latest awards to joshualevipayne

Great Question 2.8 years ago, created a question with more than 5,000 views. For Extracting Random Sequences From A Large Fasta File Using Bioperl
Teacher 2.8 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 5.3 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 5.3 years ago, created a question with more than 1,000 views. For Problem Fetching Sequences From A Bed File With Galaxy
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Where To Find Encode Dnase I Footprint Data
Student 5.3 years ago, asked a question with at least 3 up-votes. For Where To Find Encode Dnase I Footprint Data
Popular Question 5.8 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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