User: Jake

gravatar for Jake
Jake60
Reputation:
60
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Trusted
Location:
United States
Last seen:
5 months, 4 weeks ago
Joined:
3 years, 7 months ago
Email:
j*******@gmail.com

Posts by Jake

<prev • 56 results • page 1 of 6 • next >
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Normalize for changes in one direction
... Hi, I'm trying to measure RNA stability changes after knocking out a repressor RNA binding protein. I'm using 4sU to label nascent RNA and also collecting total RNA as per this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3114636/. I can then calculate RNA stability by the ratio of nascent RN ...
rnaseq limma voom written 5 months ago by Jake60 • updated 5 months ago by Aaron Lun20k
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Comment: C: Non-used samples changing number of significant genes in limma
... I tried it with both voomWithQualityWeights and voomWithQualityWeights(var.design = design). This is what the plot looks like for the second one: https://imgur.com/HDhOUhQ. The order is: ko 1 high ko 1 low ko 1 mono ko 2 high ko 2 low ko 2 mono wt 1 high wt 1 low wt 1 mono wt 2 high wt ...
written 9 months ago by Jake60
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Non-used samples changing number of significant genes in limma
... Hi, I performed polysome profiling to measure translation rate in wildtype and knockout cells. For the polysome samples I collected a monosome fraction, a low polysome fraction, and a high polysome fraction. I also collected mRNA for both wildtype and knockout. I'm interested in comparing translati ...
limma voom written 9 months ago by Jake60
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pintersect and psetdiff changed behavior
... Hi, I had code to extract exons, introns and exon-intron boundaries from about a year ago. However, when I went to re-run it I now get the following two errors. Did the behavior of these functions change? I'd like to take the range of exons in a gene (union of all isoforms) and define everything in ...
genomicranges written 16 months ago by Jake60 • updated 16 months ago by Michael Lawrence10k
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RNA-Seq metagene coverage
... Hi, I'd like to calculate RNA-Seq meta read coverage over different subsets of genes similar to the genebody coverage function in RSeQC (http://rseqc.sourceforge.net/#genebody-coverage-py). I saw a number of packages that will do this for genomic coordinates, but I'm looking for something that will ...
coverage written 2.1 years ago by Jake60
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Comment: C: RSEM expected counts to limma-voom
... They have both. I was interested in the gene quantification. ...
written 2.1 years ago by Jake60
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RSEM expected counts to limma-voom
... I'm interested in analyze some RNA-Seq data from Encode. They have posted a gene quantification file for each sample from RSEM. My understanding is that I can pass the expected counts to voom and then limma even though raw counts is more ideal. I just wanted to check that this is correct? Thanks ...
limma voom rsem written 2.1 years ago by Jake60 • updated 2.1 years ago by Gordon Smyth34k
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Answer: A: matchPWM on DNAStringSet rather than just one sequence?
... That works, but is incredibly slow once I start looping through all of my UTRs and even a few RNA binding proteins. Is there another bioconductor package or program outside that would be significantly faster? ...
written 2.2 years ago by Jake60
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matchPWM on DNAStringSet rather than just one sequence?
... I have a couple PWMs for RNA binding proteins and I also have the sequences of candidate UTRs in different groups as a DNAStringSet. I'd like to see how many of the UTRs (and which ones) in each group match a given PWM. However, it looks like the matchPWM function in Biostrings only supports a singl ...
biostrings written 2.2 years ago by Jake60
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Reorder exons on negative strand in GRanges list
... I am trying to make a fasta file of reduced exon sequences (collapse all isoforms of a gene into one transcript). I'm running into a problem where exons on the negative strand are listed in ascending order based on chromosome coordinates, but this results in the exon sequences being written in the w ...
genomicranges written 2.3 years ago by Jake60 • updated 2.3 years ago by Michael Lawrence10k

Latest awards to Jake

Popular Question 16 months ago, created a question with more than 1,000 views. For Check understanding of linear model
Popular Question 16 months ago, created a question with more than 1,000 views. For limma-voom for miRNA seq
Popular Question 16 months ago, created a question with more than 1,000 views. For rtracklayer export GRangesList as gtf and change attributes
Popular Question 16 months ago, created a question with more than 1,000 views. For coverage over specific GenomicRanges
Popular Question 16 months ago, created a question with more than 1,000 views. For ribosome profiling analysis with different dispersions
Popular Question 16 months ago, created a question with more than 1,000 views. For Ribosome profiling analysis in DEseq2/limma
Popular Question 16 months ago, created a question with more than 1,000 views. For bedtools like subtract in genomic ranges?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For genomicfeatures rsqlite database or disk is full

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