User: simplitia

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simplitia40
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Posts by simplitia

<prev • 31 results • page 1 of 4 • next >
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Comment: C: How To Do Normalization Of Two Chip-Seq Data?
... Would one have to first normalize to total reads? For example in one of the GEO set I downloaded recently the one sample had 65 million spot # whilst the other had 63 million. In this case is it necessary to first scale by total counts first? Thanks! ...
written 5 weeks ago by simplitia40
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Comment: C: How to round the "expected counts" to integers?
... Hi others might have other opinion but I think you can just simply round the numbers to nearest integer, this should be good enough. tximport power is to utilize the bootstrapping form things like kalliso but you don't have it here thus I don't think it be that much more useful but I could be wrong ...
written 7 weeks ago by simplitia40
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How reliable are the ensembl transcript isoforms?
... Hi, I was reading a recent article that mentions that there were two isoform for a particular gene they were interests in. However when I went to ensembl it turns out that there were a lot more including non protein versions. The question is I'm assuming in the ensembl transripts they are all pred ...
ensembl rna-seq isoform written 3 months ago by simplitia40 • updated 3 months ago by Astrid_Ensembl310
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GRanges: remove ranges that falls in between a larger range?
... Hi suppose I have a grange object as such, g <- GRanges(seqnames=c(rep("Chr1",3)), strand=rep("+",3), ranges=IRanges(start=c(10,2,2), end=c(24,27,30))) this produces a grange that looks like this. GRanges object with 3 ranges and 0 metadata columns: seqnames ranges stran ...
R grange rna-seq written 4 months ago by simplitia40 • updated 4 months ago by Strand NGS40
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Comment: C: How to color nodes in Cytoscape according to expression of genes? How should the
... Ok this great however does anyone know how to assign a color say grey to a node with no value ( NA ) the issue I have is the value is not availaible cytoscape will just color it with the maximum color! ...
written 5 months ago by simplitia40
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Answer: A: TMM or TPM normalized counts for visualization?
... To add to this, why not both. You can also get tpmTMM normalized- the benefit of this is to stabilize rna composition. ...
written 8 months ago by simplitia40
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STAR: Is it ok to align with an index created from genecode but count features from gtf from ensembl?
... I'm wondering if there maybe some coordinate issues as with UCSC and ensembl. I happen to have bam files which were aligned with STAR using indices that were created from gencode however, I would like to use htseq count but with gtf donwloaded from ensembl instead? thanks! A ...
alignment star rna-seq written 9 months ago by simplitia40 • updated 9 months ago by kristoffer.vittingseerup3.3k
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How to interpret exon reads from recount for version 2?
... Dear all, I'm trying to get exon by exon data matrix. I can download the data either directly from the website or through the R package. For example here is simple single sample example: download_study("DRP001219", type = "rse-exon", outdir="./data/") load(file.path( "./data/rse_exon.Rd ...
tcga rna-seq written 11 months ago by simplitia40
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Answer: A: SOAPfuse: problem in constructing database
... Hi so I had the same issue and here is what I did to fix it. 1. You need to make sure that the fasta is indeed prefix with chr which you did above by checking. I mentioned this in case some else downloaded from ensembl which does not. You can easily check this by grepping the fasta, > grep " ...
written 12 months ago by simplitia40
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Advice for gene overlap with direction between two sets.
... Hi so I have a scenario where I have 200 samples. Each samples I test for 10000 genes. I have two events, call it A and B. Whereby for each sample there can be x genes with gene.up and gene.down. What I want to do is compare if events A and B are similar: I want to see if the intersection is sig ...
R chisquare statistics written 14 months ago by simplitia40

Latest awards to simplitia

Popular Question 3 months ago, created a question with more than 1,000 views. For How to quantify PCR duplication from bam file
Popular Question 5 months ago, created a question with more than 1,000 views. For Help with BWA: how to align paired as single and then combine again
Popular Question 8 months ago, created a question with more than 1,000 views. For Create fusion transcripts with breakpoint coordinates from two genes.
Popular Question 9 months ago, created a question with more than 1,000 views. For Create fusion transcripts with breakpoint coordinates from two genes.
Popular Question 12 months ago, created a question with more than 1,000 views. For Create fusion transcripts with breakpoint coordinates from two genes.
Popular Question 12 months ago, created a question with more than 1,000 views. For Hard time trying to calculate Allele Frequency and DP from Platypus

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