User: EVR

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EVR570
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Posts by EVR

<prev • 174 results • page 1 of 18 • next >
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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 5 weeks 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 12 weeks ago by EVR570
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Comment: C: LRT test in DESeq2 giveswierd volcanplot
... https://drive.google.com/open?id=17a9st9esiDvoDzD6H5VAo-jYytvMyQ6r ...
written 12 weeks 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 12 weeks ago by EVR570 • updated 12 weeks ago by ATpoint26k
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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 6 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 2.0 years ago by EVR570 • updated 2.0 years ago by Russ460
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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 2.1 years ago by EVR570
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Comment: C: Merging bed intervals within a group
... Hi, Thanks for your reply. I tried your code, it gave the following output 11561749 14491295 ...
written 2.3 years ago by EVR570
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Merging bed intervals within a group
... Hi, I have a bed file like following: PGRP-SA-PA 11561749 11561803 PGRP-SA-PA 11561806 11561873 PGRP-SA-PA 11561875 11561925 noc-PB 14490900 14490989 noc-PB 14491004 14491065 noc-PB 14491076 14491106 noc-PB 14491117 14491182 noc-PB 14491201 14491295 I would like to ...
bedtools bed bedops written 2.3 years ago by EVR570
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Average intron length in Drosophila melagnoster
... Hi All, What is average or median intron length in Drosophila melagnoster genome. Is it 65 nts long? kindly guide me Thanks in advance. ...
drosophila intron_length written 2.3 years ago by EVR570 • updated 2.3 years ago by Malcolm.Cook1.1k

Latest awards to EVR

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Oryza Sativa Transcriptome
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Oryza Sativa Transcriptome
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Oryza Sativa Transcriptome
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Oryza Sativa Transcriptome
Popular Question 3 months ago, created a question with more than 1,000 views. For Oryza Sativa Transcriptome
Popular Question 5 months ago, created a question with more than 1,000 views. For Oryza Sativa Transcriptome
Popular Question 5 months ago, created a question with more than 1,000 views. For Counting reads within regions of interest
Popular Question 5 months ago, created a question with more than 1,000 views. For Counting reads on genome
Popular Question 5 months ago, created a question with more than 1,000 views. For Counting reads within regions of interest
Good Answer 11 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 11 months ago, created a question with more than 1,000 views. For Counting reads within regions of interest
Popular Question 11 months ago, created a question with more than 1,000 views. For Identifying full length transcripts in a transcriptome
Popular Question 11 months ago, created a question with more than 1,000 views. For Generating GTF file for de novo assmebled transcriptome
Popular Question 11 months ago, created a question with more than 1,000 views. For Quality control for AB Solid fastq files
Popular Question 11 months ago, created a question with more than 1,000 views. For All reads deposited in Undetermined indices
Popular Question 12 months ago, created a question with more than 1,000 views. For Counting reads within regions of interest
Popular Question 12 months ago, created a question with more than 1,000 views. For Identifying full length transcripts in a transcriptome
Popular Question 12 months ago, created a question with more than 1,000 views. For Generating GTF file for de novo assmebled transcriptome
Popular Question 13 months ago, created a question with more than 1,000 views. For Counting reads within regions of interest
Appreciated 17 months ago, created a post with more than 5 votes. For A: Finding UTR regions in the RNA sequencing data from a non-model organism
Popular Question 17 months ago, created a question with more than 1,000 views. For Counting reads within regions of interest
Popular Question 17 months ago, created a question with more than 1,000 views. For Identifying full length transcripts in a transcriptome
Popular Question 17 months ago, created a question with more than 1,000 views. For Generating GTF file for de novo assmebled transcriptome
Popular Question 17 months ago, created a question with more than 1,000 views. For Quality control for AB Solid fastq files
Popular Question 17 months ago, created a question with more than 1,000 views. For Splitting the y axis values in R plot

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