Biostar

986 results • Page 5 of 20

in DESeq assumes that the samples can be treated as technical replicates? Thank you. [1] Huber et al, 2002 [2] Durbin et. al, 2002 [3] http://seqanswers.com/forums/showpost.php?p=139198&postcount=8

deseq vst

updated 7.8 years ago • jiab

multiple alignment pipeline, when I looked through the original EP paper published in GR (Benedict et al. 2008), I know that the Enredo need a set of nonoverlapping GPAs(Genomic Point Anchor) as input file. So I looked the Enredo...Anchor Generation section in supplementary, it is very complicated, to derived the GPA, Gerp[Cooper et al., 2005] and BlastZ-net or Lastz-net should be included. May…

alignment

updated 12.3 years ago • Lds

message. i have tryed differents ways to generate the tree, assuming that is the problem(ape library, ete3,Phylogeny.fr ), even use a contraction of the tree given in the tutorial(to discard distance problems in tree). inputs matrix

CAFE gene expansion pyhlogeny

updated 7.3 years ago • gu.fernandezn

removed parent which in turn becomes the new root. I'm reading a newick format tree using pythons ete3 package, lets say my tree is stored in a file like this: (S1_k99_151_71_451_+:0.04173,S1_k99_259_71_451_+:0.07108,((S2_k99_3184_162148_162525_

python3 ete3 phylogenetics

updated 5.9 years ago • Moses

Hi all, I have raw sequencing datas of metagenomes and all of them are single-end reads. I would want to prolong/extend contigs. I thought of PRICE (Ruby, JG., *et al*, 2013) but it only works with paired-end reads. Do you have any recommendation on what software could I use? Thank you for your...of them are single-end reads. I would want to prolong/extend contigs. I thought of PRICE (Ruby, JG…

contigs contig-extension

updated 15 months ago • A_heath

Hello, I would like to draw a histogram with annotations like the one below. The figure is from Liu et al 2021 Genome Research (https://genome.cshlp.org/content/early/2021/12/28/gr.275453.121.full.pdf). Any pointers or package

visualization

updated 18 months ago • mikothebichon

Jeanette Baran-Gale, Michael R Erdos, Christina Sison, et al. (2013) Massively differential bias between two widely used Illumina library preparation methods for small RNA sequencing

illumina RNA-seq

updated 22 months ago • David Langenberger

I found here This image was taken from a paper from "Into the Eye of the Cytokine Storm", Tisoncik et al. 2012 thanks Assa

updated 11.2 years ago • Assa Yeroslaviz

has a simple FTP server setup (ftp://ftp.ncbi.nih.gov/) where I can access data from GEO, Genbank, et cetera. I was just curious---if one were to download **all** of that data, how much space would I need? My guess is it would be in petabytes

data

updated 6.3 years ago • breckuh

methods, different fragmentation methods, etc.) for DNA or RNA seq. I know the paper from Levin et al (Comprehehnsive comparative analysis of strand-specific RNA sequencing methods). Does somebody know about other papers

next-gen sequencing

updated 12.8 years ago • Steffi

for motif enrichment under specific high ATAC-peaks? Do I have to give the entire genome to Homer (et al.) to find motifs enriched in all peaks. Then specifically try and find what motif is under my peak of interest

ATAC-seq

updated 5.4 years ago • a.rex

in a separate plot not as a part of Waterfall using GeneVisR? Something like figure 1 in Alexandrov et al., 2016 https://d2ufo47lrtsv5s.cloudfront.net/content/sci/354/6312/618/F1.large.jpg Many thanks in advance, Rahel ![figure1

GeneVisR Mutations per MB Waterfal snp exomSeq

updated 8.0 years ago • rahel14350

for possible saturation of nucleotide substitution types on several nucleotide MSA. I know that Xia et al published an index and this is implemented in DAMBE5 However, as far as I get I should submit my MSA one by one in DAMBE, and

phylogeny alignment

updated 10.0 years ago • dago

at each position (20 bp stretch) for virus species similar to the following image by [Suzuki et al 2013][1]. ![Example Figure][2] Can you suggest a software or script that I can use to achieve this? Thanks in advance. [1]: https://1drv.ms

alignment sequence

updated 4.6 years ago • venura

Hi, I'm looking to normalize my single cell RNA-seq data using *SCnorm* (Bacher et al. 2017, *Nature Methods*). My count matrix is coerced into a SingleCellExperiment (`sce`) container with metadata (for example...genotype and treatment). The metadata was added through *scater* packer in R (McCarthy et al. 2017, *Bioinformatics*) using `colData`. I have been trying unsuccessfully to use the `col…

normalization scater metadata SingleCellExperiment

updated 6.0 years ago • TJ

cytoscape by using the python. I can export some files such as cx JSON,cx2 JSON, cytoscape.js JSON et. But how can I import them to python? even I can't read the data. I try using the networkx package to do that,but I failed. can anyone

python Cytoscape networkx

updated 7 weeks ago • 雨

Can anyone suggest a reliable parser to extract ligands (coordinates, atom types, et al.) from a PDBML or mmCIF file? I have tried BioPython (http://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ

mmCIF PDBML ligand protein

updated 2.5 years ago • GeauxEric

to determine differentially expressed genes between two conditions. We are trying to use the Pertea et al pipeline (Hisat2+Stringtie+Ballgown). Following questions: 1. should the fold change be computed using the fpkm measure

RNA-Seq Hisat2 Ballgown Stringtie

updated 6.8 years ago • nancy

I was reading this paper by Anderson et al., 2010 (http://www.ncbi.nlm.nih.gov/pubmed/21085122). I know what SNPs is very well, but I have been having difficulty understanding

genotype SNPs

updated 5.2 years ago • MAPK

Any suggestion of tools how can I do this? I attached the following example from M. R. Mansour et al., Science (80). 346 (2014) to show what I want to generate. Thanks! [Motifs located in the DNA sequence][1] [1]: https://imgur.com/a/3Fp57

ChIP-Seq

updated 7.2 years ago • Rashedul Islam

whole genome** differential binding analysis? I have checked out two review papers: 1. Shiqi Tu et al. An introduction to computational tools for differential binding analysis with ChIP-seq data 2. Sebastian Steinhauser...et al. A comprehensive comparison of tools for differential ChIP-seq analysis Based on their flow charts I have following

ChIP-Seq

updated 6.9 years ago • biopat

I am using **GeneMark-ES Suite version 4.33** for Eukaryotic gene prediction for plant genome and I am kind of stuck **command** perl gmes_petap/gmes_petap.pl --evidence protein.fa --cores 40 --sequence genome_assembly.fa --ET transcripts.gff ---------- **input files** ***protein.fa*** = a multi-fasta file having amino acid sequences from a closely related plant ***genome_assembly.f…

gene prediction genemark

updated 7.0 years ago • lakhujanivijay

Hi! I am really confused, and need some expert advice from the guys who work in NGS data analysis along with reason. Ok, the PROBLEM is: I performed peak calling using MACS and I got nice peaks(antibody used for detecting ETS factor), then I annotated these peaks to the single nearest genes in a window of 25 Kb. This was followed by De novo motif discovery and also I scanned these regions usin…

chip-seq

updated 11.3 years ago • ChIP

dge, method="TMM") dge <- estimateCommonDisp(dge) dge <- estimateTagwiseDisp(dge) et <- exactTest(dge, pair=c("ctrl", "tr")) etp <- topTags(et, n=2000000) etp$table$logFC = -etp$table$logFC Thanks a lot

RNA-Seq edgeR log fold change

updated 7.2 years ago • Sharon

filter all obtained transcripts (exonerate output file) that have poor alignment scrores. In Liang et al article (Liang C, Mao L, Ware D, et al. Evidence-based gene predictions in plant genomes[J]. Genome research, 2009, 19(10): 1912-1923

genome alignment

updated 9.2 years ago • Ginsea Chen

39; depending on sample number. Also can be adapted to replicated samples, see'?DGEList'. d et <- exactTest(d, pair=(1:2),dispersion=bcv^2) #exactTest(RG, pair=(1:2),dispersion=bcv^2) et top <- topTags(et) top cpm(RG)[rownames(top), ] #Check...the individual cpm values for the top genes: summary(de <- decideTestsDGE(et)) #The total number of DE genes at…

edger rna-seq bacteria ion-torrent

updated 10.7 years ago • biotech

Hi, I am trying to perform DEG analysis without replicates while referencing EdgeR User's Guide(page23). I have 3 replicates but I want to compare each sample (cont3 vs sample1). > library(edgeR) > packageVersion("edgeR")[1] ‘3.30.3’ > count <- read.table("3vs1.txt", + sep = "\t", header = T, row.names = 1) > head(count…

R RNA-Seq

updated 4.5 years ago • Aki

canonical nucleic acid structures, such as G-quadruplexes, in the genome and transcriptome (Chambers et al., Nature Biotechnology 2015, DOI: 10.1038/nbt.3295; Kwok et al., Nature Methods 2016, DOI: 10.1038/nmeth.3965; Hänsel-Hertsch...et al., Nature Genetics 2016, DOI: 10.1038/ng.3662). * Identification and mapping of modified bases, such as cytosine and thymidine...modifications, and understand…

Epigenetics Chemical-biology Sequencing

updated 21 months ago • dariober

Hi guys, I would you to revise my edgeR code since it's possible I missed something important because being quite new on this. Thanks, Bernardo ``` ############################################################ #htseq-count stats ############################################################ # rRNA and tRNA will be discarded in counts file because the arbitrary mapped reads to these regions # NOTE…

edgeR rna-seq

updated 3.3 years ago • biotech

Hi all, I've used MEGA6 to infer the ancestral states of a given site. The MEGA5 citation ([Tamura et al., 2011][1]) states that ancestral sequences can be reconstructed. However, I am unable to find how to view the inferred ancestral

phylogenetics MEGA

updated 2.4 years ago • tim_mci

Journal of Sciences. 2021; 41(4):898. https://10.20892/j.issn.2095-3941.2018.0055" to **[1] Faehling et al. 2021. JS, 41(4):898.** using regular expression

Linux grep

updated 3.2 years ago • shabbas12

Hi, I'm reading [Rezola et al][1] in PlosOne. I was wondering whether elementary flux modes are essentially the same thing as vectors in a matroid. Not

metabolism systems-biology

updated 3.1 years ago • russhh

Hi there! My question is pretty straightforward: **are those probes described on [Chen et al., 2012][1] paper for Illumina's 450K methylation array still valid for the EPIC version?** If not, would there be an updated list

illumina microarrays methylation

updated 3.2 years ago • dodausp

Hello, I know that a database of miRNA:mRNA interactions scored by mirSVR (Betel et al. 2010) exists on the microRNA.org web resource. However, I wish to calculate mirSVR scores for custom miRNA and mRNA sequences

miRNA miRanda mirSVR Target Prediction

updated 8.7 years ago • Thomas

I have read some papers, mainly "Basic statistical analysis in genetic case-control studies” (Clarke et al. 2011, Nature Protocols 6: 121-33),but I am not sure which input to follow. Thanks

plink

updated 10.9 years ago • tom.d.brocklehurst

scRNA-seq data prepared with Smart-seq2 protocol. I have been using HISAT-StringTie-Ballgown(Partea et al. 2016) for my bulk RNAseq data. For scRNAseq I have aligned& assembled transcripts with HISAT-StringTie. Yet, I believe

single-cell RNAseq methods normalization

updated 4.2 years ago • asumani

percentage of mapped reads and they also have very low number of mapped reads for some samples (Reid et al., J Biological Chemistry 2012 and de Klerk et al., NAR 2015). Still I am not sure if this is the most common case. Some details on

ribosome-profiling ribosome-footprinting mapping

updated 2.5 years ago • laura.fancello

calculating tools to help inform the trade off between depth and biological reps (Scotty ([Busby, et al 2013][1]), RNASeqPower ([Hart, et al 2014][2]) and looking at as much literature on the topic as I can. A lot of the focus is on poly-A enriched

sequencing RNA-Seq

updated 3.0 years ago • createanotherone

I would like to understand what the meaning of 'tag is in the following paragraph. Does it mean "correlated with" or does it somehow act on the tagged gene? > The supplementary meta-analyses confirmed one additional independent locus that showed genome-wide significant association with CM (rs7412746 on chromosome 1q21; Amos et al., 2011), which was not included in our previous meta-analys…

interpretation variant

updated 7.3 years ago • andrewl

A**. Epigenetic Memory: The lamarckian brain, ***EMBO J***. 2014 Epub ahead of print - Benito, E. et al. **Fischer, A**. Reinstating transcriptome plasticity and memory function in models for cognitive decline, ***Journal of Clinical...Investigation***, in press - Stilling, et al. **Fischer, A**. De-regulation of gene expression and alternative splicing affects distinct cellular pathways in the…

NGS epigenetics Neuroscience

updated 2.3 years ago • Gjain

and international research groups. Relevant recent publications from our group include Doyle et al, Frontiers in Cell & Dev Bio (2022), Conway et al, Molecular Cell (2021), Tamburri et al, Molecular Cell (2020), and Conway et al

Post-doctoral Fellow UCD Level or 2 1 Research

updated 23 months ago • rachel.kelly1

to work with a group of international leaders in the field of translational research (e.g. Kraiczy et al. Mucosal Immunology 2016, Baud A et al, PLoS genetics 2017, McKinney EF et al Nature 2015) and apply cutting edge computational

next-gen R Bioconductor

updated 20 months ago • anke

this channel . The protocol for calculation based on the collective diffusion model proposed by Zhu *et al*. I am not able to get how I can do this . Can Someone help me in this regard. Thanks

permeability Osmotic transport Water

updated 13 months ago • Peerzada

genetic variant annotator I should use for mutation in drosophila. I found that William P. Gilks et al. used SNPeff v4.1 (https://doi.org/10.12688/f1000research.9912.3), but the problem is that its not working on the server

annotator Drosophila mutations annotation functional genetic variant

updated 20 months ago • Kirill

event given a hybrid individual in an admixed population. I am aware of an approach used in vonHoldt et al., 2022 (https://www.science.org/doi/10.1126/sciadv.abn7731), but they use total genome length in cM, which is not available

event Inference Hybrids Generations since admixture

updated 23 months ago • Matteo

allele-frequencies coming from Hartl and Clark (2007), and the allele-counts method by Karlsson et al. (2007). Would anyone be able to tell me what are pro's and con's from experience of one method versus the other? Adrian

NGS FST popgen

updated 3.2 years ago • Adrian Pelin

I am following the paper [Lieberman-Aiden,van Berkum et al., 2009][1]. in this paper figure number 4 shows fractal and equilibrium globule structure which related with chromatin...I am following the paper [Lieberman-Aiden,van Berkum et al., 2009][1]. in this paper figure number 4 shows fractal and equilibrium globule structure which related with chromatin structure

Hi-C fractal-globule chromosomal-territory

updated 3.3 years ago • Raghav

to find significantly expressed genes from these data using z-score as in the article by [\[Hart et al\]][1] but my data is not normally distributed. I was wondering if there is another method to find the active / significantly

RNA-Seq DEG

updated 4.6 years ago • jabbari.parnian

Hi there!!! While reading to an article (*Chatelier et. al., 2013*) related to metagenomics, I have come accross two terminologies: `Gene count` and `Gene richness`. Are they same? They...Hi there!!! While reading to an article (*Chatelier et. al., 2013*) related to metagenomics, I have come accross two terminologies: `Gene count` and `Gene richness`. Are they same? They have

metagenomics wgs

updated 4.5 years ago • dpc

Hello, I have downloaded the processed data of gene expression of a scRNA-Seq experiment (Tirosh et al, 2016). In their supplementary data they have listed marker genes for each cell type. But when I search these markers in...Hello, I have downloaded the processed data of gene expression of a scRNA-Seq experiment (Tirosh et al, 2016). In their supplementary data they have listed marker genes fo…

RNA-Seq

updated 4.7 years ago • jabbari.parnian

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