User: EVR

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EVR570
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570
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Trusted
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Earth
Last seen:
1 week, 1 day ago
Joined:
5 years, 5 months ago
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Posts by EVR

<prev • 177 results • page 1 of 18 • next >
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Genomic intervals to transcriptomic intervals
... HI, I have a set of bed intervals from human genome and I need to convert the genomic intervals to transcriptomic intervals. Any guidance would be highly appreciated. Thanks in advance. ...
bed rna-seq written 11 weeks ago by EVR570
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Comment: C: If loop in snakemake
... for second issue, just the change the name of the rule ...
written 5 months ago by EVR570
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Statistically overrepresented gene types from Differentially expressed genes.
... Hi, I have DESeq2 results from RNA-seq after comparing Control and Treated samples and obtained a list of differential expressed genes(DEG). My DEG includes genes of a different type. i.e. protein-coding, lincRNA, snoRNA, tRNAs etc., I want to identify statistically overrepresented gene types fr ...
enrichment next-gen gene-types rna-seq written 5 months ago by EVR570 • updated 5 months ago by i.sudbery8.4k
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Comment: C: RNA half-life calculation using SlamDunk
... Hi @lech.kaczmarczyk @Caleb, Were you people able to compute RNA-half lives from SLAMdunk pipeline. If yes, I would be grateful, if you could share the pipeline how you achieved it. Thanks in advance. ...
written 9 months ago by EVR570
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Answer: A: Filter transcripts based on CDS length
... HI, You can group the data.frame based on genestabelId and later take max(CDS Length) which will provide what u want. > setDT(data.frame)[, .SD[which.max(CDS Length)], by=Gene stable ID] ...
written 11 months ago by EVR570
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Comment: C: LRT test in DESeq2 giveswierd volcanplot
... https://drive.google.com/open?id=17a9st9esiDvoDzD6H5VAo-jYytvMyQ6r ...
written 11 months ago by EVR570
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LRT test in DESeq2 gives weird volcano plot
... Dear All, I am using LRT(with full model and reduced model) to compute the differential expressed genes. But when I generate the volcanoplot using ggplot, I am getting the following figure where point converged towards the summit. I also came across similar plot in bioconductor forum when LRT was u ...
deseq2 volcanoplot rna-seq lrt written 11 months ago by EVR570 • updated 11 months ago by ATpoint36k
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Comment: C: How to determine if SRA file is single or paired end?
... Hi @davedeto, I liked your python script to find the single-end or paired-end. I am very new to pytthon and in my case I have fastq files generated from illumina sequencing. In my case, the paired-end reads name are samplename_1_sequence.txt.gz and single-end reads name samplename_sequence.txt.gz. ...
written 14 months ago by EVR570
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Identifying miRNA, RNA-binding sites in UTRs
... HI all, I have UTRs regions of many transcripts of a non-model organism of my interest and I would like to identify the miRNA, RNA binding sites and post transcriptional regulatory elements in the UTRs. Can you suggest a database where can I download the target sequences. Thanks in advance ...
minra rna-binding protein utrs written 2.7 years ago by EVR570 • updated 2.7 years ago by Russ470
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Answer: A: Visualization of Gene Ontology using bubble plot.
... HI Agamy89, I generally use [REVIGO][1] for visualizing the GOs. The best part of revigo is that all its plots are generated in R and you can download the R script and work on it to suit your needs [1]: http://revigo.irb.hr/ ...
written 2.7 years ago by EVR570

Latest awards to EVR

Great Question 15 days ago, created a question with more than 5,000 views. For High Sequence Duplication levels in FastQC
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Counting reads on genome
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Counting reads on genome
Popular Question 4 months ago, created a question with more than 1,000 views. For Detecting the peaks from RNAseq data
Popular Question 4 months ago, created a question with more than 1,000 views. For Counting reads on genome
Popular Question 9 months ago, created a question with more than 1,000 views. For Oryza Sativa Transcriptome
Popular Question 10 months ago, created a question with more than 1,000 views. For Oryza Sativa Transcriptome
Popular Question 10 months ago, created a question with more than 1,000 views. For Oryza Sativa Transcriptome
Popular Question 10 months ago, created a question with more than 1,000 views. For Oryza Sativa Transcriptome
Popular Question 11 months ago, created a question with more than 1,000 views. For Oryza Sativa Transcriptome
Popular Question 13 months ago, created a question with more than 1,000 views. For Oryza Sativa Transcriptome
Popular Question 13 months ago, created a question with more than 1,000 views. For Counting reads within regions of interest
Popular Question 13 months ago, created a question with more than 1,000 views. For Counting reads on genome
Popular Question 14 months ago, created a question with more than 1,000 views. For Counting reads within regions of interest
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: Finding UTR regions in the RNA sequencing data from a non-model organism
Popular Question 20 months ago, created a question with more than 1,000 views. For All reads deposited in Undetermined indices
Popular Question 20 months ago, created a question with more than 1,000 views. For Quality control for AB Solid fastq files
Popular Question 20 months ago, created a question with more than 1,000 views. For Generating GTF file for de novo assmebled transcriptome
Popular Question 20 months ago, created a question with more than 1,000 views. For Identifying full length transcripts in a transcriptome
Popular Question 20 months ago, created a question with more than 1,000 views. For Counting reads within regions of interest
Popular Question 21 months ago, created a question with more than 1,000 views. For Counting reads within regions of interest
Popular Question 21 months ago, created a question with more than 1,000 views. For Generating GTF file for de novo assmebled transcriptome
Popular Question 21 months ago, created a question with more than 1,000 views. For Identifying full length transcripts in a transcriptome
Popular Question 21 months ago, created a question with more than 1,000 views. For Counting reads within regions of interest
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: Finding UTR regions in the RNA sequencing data from a non-model organism

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