User: simplitia

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simplitia40
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Posts by simplitia

<prev • 33 results • page 1 of 4 • next >
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Answer: A: Checking integrity of SRA downloaded fastq files
... I ran into the same issue in that the vdb-validate does not work if you are downloading the fastq files without prefetching the sra, you are left with only a fastq file which cannot be validated. It strange that the there isn't a simple checksum that is provided, may be we can get the admin to incl ...
written 11 weeks ago by simplitia40
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Where can I get the GTex equivalent to rnaseqv2 Level3 RSEM_genes?
... Hi I want to compare TCGA lung cancer to normal lung in GTex. Currently I download expected_counts/raw counts from Gdac firehouse. My understanding is that this is from the Tcga Rnaseqv2 Level3 Data pipeline. However Gdac does not have GTex data. My question, do you know where I can download GT ...
tcga rna-seq rsem written 12 weeks ago by simplitia40
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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 4 months 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 5 months 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 6 months ago by simplitia40 • updated 6 months ago by Astrid_Ensembl330
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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 7 months ago by simplitia40 • updated 7 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 8 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 12 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 12 months ago by simplitia40 • updated 12 months ago by kristoffer.vittingseerup3.4k
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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 14 months ago by simplitia40

Latest awards to simplitia

Popular Question 6 months ago, created a question with more than 1,000 views. For How to quantify PCR duplication from bam file
Popular Question 8 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 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 Create fusion transcripts with breakpoint coordinates from two genes.
Popular Question 16 months ago, created a question with more than 1,000 views. For Create fusion transcripts with breakpoint coordinates from two genes.
Popular Question 16 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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