User: simplitia

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simplitia30
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Posts by simplitia

<prev • 26 results • page 1 of 3 • next >
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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 27 days ago by simplitia30
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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 7 weeks ago by simplitia30 • updated 7 weeks ago by kristoffer.vittingseerup2.6k
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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 3 months ago by simplitia30
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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 5 months ago by simplitia30
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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 6 months ago by simplitia30
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Comment: C: Understanding FANTOM5 CAGE fields
... great thanks that is super helpful. Here is couple of followup questions. 1. So using that example above, p1@LINC200277 is about 29 bp in width. So does that mean the TSS for this gene can be within any of the 29 bp in this range? 2. Moreover if its range how is it only a single digit 0bp_to_ ...
written 9 months ago by simplitia30
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Understanding FANTOM5 CAGE fields
... Hi recently I downloaded data from FANTOM5 Phase 2.0 ( http://biomart.gsc.riken.jp/ ) with the goal of figuring out TSS sites, however I cannot seem to find any documentations on this. For example, I downloaded FANTOM5 Phase 2. I'm a bit confused, ![enter image description here][1] [1]: http ...
transcription rna-seq tss written 9 months ago by simplitia30 • updated 9 months ago by kristoffer.vittingseerup2.6k
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Comment: C: from .BAM to .BAI using samtools
... thanks this is useful. Do you know what is the optimal way of setting -j ? Without setting it does it just default to max cores? Or should I set it to something total core minus 1. That is if I have 8 then I will just set it to 7? thanks. ...
written 10 months ago by simplitia30
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Help convert GDC exploration url to API download?
... Hi all, I have the search query from GDC https://portal.gdc.cancer.gov/exploration?cases_size=10000&facetTab=mutations&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.available_variation_data%22%2C%22value%22%3A%5B%22ssm ...
portal mutation gdc written 11 months ago by simplitia30 • updated 10 months ago by Biostar ♦♦ 20
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Comment: C: How to recreate FASTQ from BAM
... this looks promising. I'm going try this and report back. Thanks. ...
written 11 months ago by simplitia30

Latest awards to simplitia

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Create fusion transcripts with breakpoint coordinates from two genes.
Popular Question 4 months ago, created a question with more than 1,000 views. For Create fusion transcripts with breakpoint coordinates from two genes.
Popular Question 4 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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