Biostar

986 results • Page 6 of 20

two hydrogen bonds. However in the paper "A computer scientist's guide to molecular biology" by Kari et al. [1], at the end of 2nd section, it says In RNA, C is complementary to G, and U is complementary to A and G. ... except that in RNA U takes

rna

updated 13.0 years ago • Sefakilic

I've got a few questions: I'd like to build supertranscripts using Corset & Lace (Davidson et al. 2017). How does one go about annotating these for later differential expression analysis? How do you analyse the quality...per assembled transcript, longest coding region, or by shared alignment [Gilbert 2019, Davidson et al. 2014]) If anyone has some insights into this, I'd be very thankf…

assembly RNA-Seq

updated 4.6 years ago • ponganta

several PhD students, and three senior scientists. Recent publications: Yang Chengran et al, Nat Neurosci. 2021 Sep;24(9):1302-1312 Laura Ibanez, et al. Genes (Basel). 2021 Aug 15;12(8):1247 Claudia Olive, et al. J Alzheimers...Dis. 2020;77(4):1469-1482 Umber Dube et al, Nat Neurosci. 2019 Nov;22(11):1903-1912 Qualifications • A PhD in Neurogenetics, Neuroscience, Genetics, Bioinform…

QTL

updated 2.7 years ago • doscar

7q11.23 that display a striking combination of shared and symmetrically opposite phenotypes (Adamo et al. *Nature Genetics, *2015; *News and Views *by Urban and Purmann in the same issue). We discovered that iPSC and early developmental...interactive, multi-national team at the cutting edge of cell reprogramming and neurobiology (Adamo et al. *Nature Genetics* 2015; *News and Views* by Urban and …

ngs epigenetics

updated 2.3 years ago • ivivek_ngs

Hello, hoping I can get some help or insights to good tutorials to understand further as I'm pretty new. Please let me know if this question is even possible: Q1) I'm trying to follow Shmakov et al. CRISPRicity pipeline to adapt it for a different purpose and am having trouble implementing some of the methods a) "The translated prokaryotic database was searched with PSI-BLAST (95) using the pre…

blast psi-blast pssm

updated 22 months ago • ceosikpa

I am running** bcv <- 0.4 y <- DGEList(counts=df_data, group=df_metadata$CoreLabID) et <- exactTest(y, dispersion=bcv^2) > View(et$table) > structure(list(logFC = c(0, -0.67280976110796, -0.190706878123648, > 0, -1.06592239047733...Gene2", "Gene3", "Gene4", "Gene5", > "Gene6"), class = "data.frame") > &gt…

R edgeR expression rna-seq differential

updated 3.6 years ago • mohammedtoufiq91

each step, but also popular software used and major challenges faced. http://epigenie.com Bailey T, et al.(2013) **Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data**. PLoS Comput Biol 9(11): e1003326. http://www.ploscompbiol.org

ChIP-Seq peak-calling sequencing

updated 22 months ago • dnaseiseq

career stage, from some established researchers in bioinformatics/computational biology. de Ridder et al (2013) Don't Wear Your New Shoes (Yet): Taking the Right Steps to Become a Successful Principal Investigator: http://www.ploscompbiol.org

career

updated 22 months ago • Casey Bergman

with bowtie 2 tool and new to this field thus trying to reproduce the work of Memczak, Sebastian, et al. "Circular RNAs are a large class of animal RNAs with regulatory potency." *Nature* 495.7441 (2013): 333-338. Can anyone please

RNA-Seq

updated 2.3 years ago • neha 114

de-novo-assembly/software/pipelines/latest/output/generating) neither from Weisenfeld et al. 2017 Genome Research 27:1–11. Thanks a lot in advance Milos

gap_length_estimation 10X_Genomics genome_assembly Supernova_assembler

updated 3.6 years ago • MH85

I don't know if I can assign the same sigma factor to that particular motif as predicted in Nicholas et. al, 2012, as I'm working with the same bacteria Bacillus subtilis. if anyone has used it, please help me with this. Thank you

CLUSTERS TREEMM PROMOTER

updated 3.7 years ago • madhujamano

C contact matrix) for each cell line and each cell from this single cell Hi-C experiment? Ramani, V. et al. Massively multiplex single-cell Hi-C. Nat Methods 14, 263- 266 (2017). - Shendure lab https://www.ncbi.nlm.nih.gov/pmc/articles

hi-c single-cell

updated 5.5 years ago • somnath52

make the script run? The python script is below: #!/usr/bin/python import csv from ete3 import NCBITaxa ncbi = NCBITaxa() def get_desired_ranks(taxid, desired_ranks): lineage = ncbi.get_lineage(taxid) names

python

updated 5.8 years ago • Ming

DGEList(counts = cpm_data, group = group) y <- calcNormFactors(y) y <- estimateDisp(y) et <- exactTest(y) results_edgeR <- topTags(et) results_edgeR$table logFC logCPM PValue FDR hsa-miR-10395-3p 2.1245133 2.067156

FDR differential-gene-expression edgeR miRNA

updated 9 months ago • AngAdd

to a classical phylogenetic approach. I want to take an approach similar to the study by [Fay et al. (2019)][1] however I have questions regarding the validity of using TreeMix on polyploid strains. Yeasts have various ploidy...are tetraploid, and therefore I made tetraploid variant calls. On the other hand, I can see that Fay et al. used `sample_ploidy=1` in their pipeline. The standard treemix …

ploidy admixture SNP TreeMix

updated 15 months ago • Michael

counts=d,group=g) dge <- estimateCommonDisp(dge) dge <- estimateTagwiseDisp(dge) et <- exactTest(dge) topTags(et, n=100000

edgeR

updated 8.5 years ago • biolab

estimateCommonDisp(dge) dge <- estimateTagwiseDisp(dge) dge <- estimateTrendedDisp(dge) et <- exactTest(dge, pair=c("Control", "Tumor")) etp <- topTags(et, n=100000) write.csv(etp$table, "dge.csv") Thanks

RNA-Seq

updated 7.1 years ago • Tania

calcNormFactors(dge) dge <- estimateCommonDisp(dge) dge <- estimateTagwiseDisp(dge) et <- exactTest(dge, pair=c("WT", "Mut")) etp <- topTags(et) etp$table$logFC = -etp$table$logFC

RNA-Seq edgeR

updated 7.2 years ago • Sharon

which are composed of independent subpools that we amplify using the primers published in Sanson et. al (https://www.nature.com/articles/s41467-018-07901-8). These are 6 primer pairs. We are now in a situation where we want to order

wet-lab

updated 8 weeks ago • gernophil

in his talk: #### Code, sweat, and tears: how the OSCA sausage was made When: April 03, 2023, 3 PM ET Where: https://harvard.zoom.us/j/97173440183?pwd=eHI1ODRub0p5NGNEZncwU0lURlJjdz09

scrna-seq

updated 21 months ago • ATpoint

if those interactions are modified by any mutation. From now on I've been using the db of Shagni *et al*. 2015 but this is not enough and I don't know where to find the data Thank you all

PPI

updated 2.4 years ago • albert.castella.teruel

I have this variant (rs17863783) from [Visscher et al. 2013 ][1], where they reported alleles as `A,C` for this variant. ![enter image description here][2] However, when I checked this...I have this variant (rs17863783) from [Visscher et al. 2013 ][1], where they reported alleles as `A,C` for this variant. ![enter image description here][2] However, when I checked this in

GATK VCF

updated 2.3 years ago • MAPK2

a case study using different electrostatic potentials. Hou X1, Du J, Zhang J, Du L, Fang H, Li M.X et al

Partial-Charge Drug-Designing Ligand-Preparation

updated 2.5 years ago • dasdevashishdas

I need to perform profile-profile alignments of protein sequences using PROFMAKE/PROFANAL (*Gribskov et al. Profile analysis: Detection of distantly related proteins*) and Dirichlet Mixtures. If there was a library/package that

profile alignment python C/C++

updated 8.3 years ago • a.abnousi

the adjusted P value? I thought it might be so given Figure 2 in the original enrichR paper (Chen et al, 2013) but I haven't taken a statistics course yet despite being a first year in a biomedical PhD program. Thank you for all

enrichR statistics significance RNA-Seq

updated 4.7 years ago • kathryn.eckartt

to work. I want to be able to see LD and a SNP's genomic position at the same time. I use LocusZoom et al. for visualizing GWAS results, but I don't think it will work for genotypic data. Has anyone found a way around this problem

ld haploview hapmap

updated 10.8 years ago • adkinsae

Hello, I've ran a genome scan with the software LFMM (frichot et al. 2013) and under all reasonable number of latent factors (k), I get a very high genome inflation factor (2.8-3.3). I'm not sure...Hello, I've ran a genome scan with the software LFMM (frichot et al. 2013) and under all reasonable number of latent factors (k), I get a very high genome inflation factor (2.8-3.3). I'm not sure what

next-gen genome genome scan GIF false positives

updated 4.5 years ago • age00

not find the paper describing it. The paper cited mostly "Indexing Compressed Text" by Ferragina et al. 2004 focus on the analysis of memory footprint and query time analysis, but not the running time of building FM Index

FM-Index BWA Bowtie2 bowtie alignment

updated 8.4 years ago • Chen

markers have no p value threshold but logfc.threshold = 0.25 and min.pct = 0.2. According to Reimand et al. 2019 (Nature Protocols; 14:482-517), partial ranked gene lists should be analyzed using pathway enrichment analysis. How

GSEA pathway scRNAseq

updated 3.8 years ago • aa123

mRNA splice variant called ARV-7 from the Metastatic Prostate Cancer, SU2C/PCF Dream Team (Robinson et al., Cell 2015) data in cbioportal.org. The downloaded data looks like this SampleID AR 1115153 3.0771 1115154 1.4149 1115156

gene mRNA

updated 6.9 years ago • kulani.s91

Use one of the newer 'integration' approaches (e.g. as implemented in Seurat's IntegrateData (Butler et al.)? Thanks

single cell scRNA

updated 5.0 years ago • jhb80

for EWS-FLI1 induced malignancies. **Most recent relevant publications**: - Schwentner R, et al. EWS-FLI1 employs an E2F switch to drive target gene expression. Nucleic Acids Res. 43(5):2780-9. PMID:25712098 - Tomazou-EM...et al. (2015). Epigenome mapping reveals distinct modes of gene regulation and widespread enhancer reprogramming by the oncogenic...fusion protein EWS-FLI1. Cell Reports, 1…

systems-biology

updated 2.1 years ago • Christian

for synthetic DNA and RNA standards (`seqins`) that can be used as spike-in controls. Deveson et al: http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3957.html > DNA Controls > > We have developed a set...gt; reference genome, which allows them them to be partitioned for > parallel analysis. Hardwick et al: http://www.nature.com/nmeth/journal/vaop/ncur…

RNA-Seq assay spike-in

updated 21 months ago • GenoMax

I am conducting GWAS QC and would like to exclude regions of high linkage disequilibrium (LD) during pruning of my data (which is in GRCh38). **Does anyone know where I may find a list of high LD positions in build 38? ... or how may I map the positions listed in *https://genome.sph.umich.edu/wiki/Regions_of_high_linkage_disequilibrium_(LD)* to build 38?** I also found a list in build 37 in …

linkage disequilibrium GWAS GWAS QC build 38 LD

updated 4.4 years ago • yy237

contribution of this pathway to cognitive ageing, MCI and risk for AD in humans. References: Lu T, et al. (2014). Nature 507:448-54. Nicodemus KK, et al. (2014). JAMA Psychiatry [in press]. 2\. **Supervisor**: Kristin Nicodemus (CCACE member Genetics...learning to assess the contribution of this pathway to cognition in humans. References: Darnell JC, et al. (2011). Cell 146:247-61. Nicodemus KK,…

SNP R

updated 22 months ago • nicodemk

Timing of Glucocorticoid Treatment. Immunity 2017, 47(2):298-309 (PMID: 28801231) - Sung MH et al. Genome-wide footprinting: ready for prime time? Nature Methods 2016 (PMID: 26914206) - Sung MH et al. DNase footprint signatures...by factor dynamics and DNA sequence. Molecular Cell 2014 (PMID: 25242143) - Kieffer-Kwon KR et al. Interactome maps of mouse gene regulatory domains reveal basic prin…

next-gen-sequencing RNA-seq ATAC-seq

updated 19 months ago • mia86sung

I'm using edgeR for DE analysis of RNASeq data. I've been using manual filtering suggested in the EdgeR manual till now. I followed genefilter package and tried to chose a theta that has the optimal number of rejections. Basically this is what I did: run edgeR once for the data set, then use the p-value results for genefilter calculations and plots. ``` dge <- DGEList(counts=counts[,!is.…

genefilter R RNA-Seq edgeR

updated 2.7 years ago • cafelumiere12

very helpful to receive suggestions regarding how to deal with these "chimeric" codes such as 'IQ', 'ET', and 'EGIPQ'. I've read that researchers often keep just one ID per gene, but I aim to keep as much info as possible. ![example of chimeric

COG

updated 21 months ago • Constanza

Hi, I am trying to filter out bad probesets using mas5 present/absent calls. But now I want to map those probes to genes. I know there are updated mappings for example, in the custom CDFs provided by Dai et al (http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp) -- how do I pull the probeset2gene...probes to genes. I know there are updated mappings for …

bioconductor affymetrix

updated 2.0 years ago • Brian Tsai

please someone tell me if I should use `-r` or not? If I should use, then why in protocol Trapnell et al. didn't mentioned anything about `-r`? Thank you

RNA-Seq tophat next-gen-sequencing

updated 2.5 years ago • Angel

to run using both MPI and Beagle. But I am not sure. Any idea? The same question actually for PHYML (et cetera) Thanks Arjen

mrbayes kepler

updated 3.3 years ago • Arjen Ten Have

There are a number of articles on ohnologs (genes that are duplicated via whole genome duplication). Most of them cite the original publication where they initially identify the ohnologs (Nakatani et. al., http://genome.cshlp.org/content/17/9/1254.long#fn-1). However, I am unable to get such a list from the supplementary data of...Most of them cite the original publication where they initially id…

ohnolog WGD

updated 2.8 years ago • Ömer An

genome assembly quality. So far we've compared basic statistics (number of contigs, bases, N50 et cetera), and we have aligned a set of unigenes to see whether those can be found back and show concordance over the different

genome assembly De-novo

updated 3.0 years ago • Coryza

I was reading this paper by Powell et al ( http://www.nature.com/nrg/journal/v11/n11/full/nrg2865.html ). They have described the instances where IBD values are...I was reading this paper by Powell et al ( http://www.nature.com/nrg/journal/v11/n11/full/nrg2865.html ). They have described the instances where IBD values are calculated

IBD

updated 8.6 years ago • MAPK

how to make a plot ![Plot][1] like this, which is from an ATAC-Seq methods paper (Buenrostro, J.D., et al. doi: 10.1002/0471142727.mb2129s109) of RNA-Seq Data I'm not sure how I can get the insert size and then the normalized read

RNA-Seq

updated 8.1 years ago • dec986

I am trying to understand the Out of Africa model proposed by Gutenkunst et al. (2009) and how to reproduce it using ms (Hudson, 2002). I think all the relevant information is in the Supplementary materials

genome ms msms simulation

updated 7.8 years ago • GabrielMontenegro

Hello, According to a review by D Sims et al [1], the required average mapped depth is 35× in order to detect heterozygous SNVs and indels in resequencing studies. I...Hello, According to a review by D Sims et al [1], the required average mapped depth is 35× in order to detect heterozygous SNVs and indels in resequencing studies. I wonder

sequencing alignment

updated 8.0 years ago • michaela_boell

Hi, I'm familiar with the kinome tree from the Manning et al paper and I'd like to be able to make use of such a tree to identify kinases that are related to a kinase of interest. As far

tree sequence

updated 13.8 years ago • Rajarshi Guha

Hi everyone, It's my first time with biopython, and I want to use a method described in a paper I'm interested in ( Emily Clough *et al* 2014) as the Bio. Site.search_pwm method. I was looking directly in the Biopython documentation : http://biopython.org/DIST...with biopython, and I want to use a method described in a paper I'm interested in ( Emily Clough *et al* 2014) as the Bio. Site.search…

biopython

updated 8.5 years ago • Rox

maybe they wrote a custom script. Any help is much appreciated. Thanks! ![Image panel D from Villar et al.][1] [1]: http://www.cell.com/cms/attachment/2051100647/2059254405/gr2.jpg

heatmap R

updated 5.5 years ago • urjaswita

986 results • Page 6 of 20

Recent Votes

Answer: Using t test to compare z-scores from RNA expression data

Comment: Premade RNA-seq pipeline or custom

A: Rna Composition Bias In Rna-Seq Analysis

Rna Composition Bias In Rna-Seq Analysis

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