Biostar

986 results • Page 3 of 20

driven research that aims developing algorithms for a wide range of applications (e.g. Yang et al., Bioinformatics 2010; Yang et al., BMC Genomics 2014; Yang et al., Genome Medicine 2015), to hypothesis-driven investigation...problems where the main goal is the discovery and advancement of biological knowledge (e.g. Asangani et al., Nature 2014; Henzler et al., Nature Communications 2016; Katernd…

Postdoc Deep-Learning

updated 23 months ago • yangliz5

genotyping using low coverage whole genome re-sequencing data? Currently I can find MSG (Andolfatto et al 2011) and MPR (Xie et al 2010) are the two tools which uses HMM to genotype from a very low coverage resequencing (<1x coverage...Alternative tool is skim-based GBS (Bayer et al 2016) which basically use sliding window approach. It would be great if you can point out other tools availa…

sequencing SNP genotyping GBS

updated 2.4 years ago • Gvj

In Jellyfish's original paper(Marcais et al, Bioinformatics 2011), it says that "counting kmers up to 31 bases in length". But on the other hand, in other papers such as...In Jellyfish's original paper(Marcais et al, Bioinformatics 2011), it says that "counting kmers up to 31 bases in length". But on the other hand, in other papers such as KMC2...Deorowicz et al, Bioinformatics 2015), Jellyfi…

jellyfish kmer kmer counting Jellyfish

updated 7.7 years ago • Chen

along with new computational resources for benchmarking differential expression (Germain et al., Nucleic Acids Research 2016). We recently elucidated the Polycomb-dependent dysregulation in transcription factor...networks underlying glioblastoma multiforme (Signaroldi, Laise et al., Nature Communications 2016), and defined new benchmarks for the disease-modeling field through the thus far largest…

ChIP-Seq RNA-Seq bioinformatician

updated 21 months ago • ivivek_ngs

to calculate the local internal stability of several RNA duplexes in siRNA, as described in Khvorova et al. (2003) based on (delta G) calculations according to Freier et al (1986). I also want to calculate local stability at other temperatures...than 37 degrees (not every bug lives at 37 degr. C) to achieve plots similar to Figure 2 in Khvorova et al. How well does the stability calculation trans…

rna

updated 8.6 years ago • Michael Dondrup

like to know which words are under-over represented in both, but using a high Markov model ([Rocha et al.]) led to a powerless statistic tests, because of low counts, when using bigger k lengths. Any of the friends have a suggestion...of a different or robust model to access this comparison? Thanks in advance. Paulo [Rocha et al.]: http://genome.cshlp.org/content/11/6/946.full

genomes k-mers statistics

updated 2.3 years ago • schlogl

salary plus generous benefits dependent on experience. **Representative Publications** Kim et al., ***Nature***. PMID: 35768511 Gaudet et al., ***Science***. PMID: 34437126 Huang et al., ***Nature***. PMID: 34040255 Huang et al., ***Curr Opin Immunol...PMID: 31176142 Wu et al., ***Elife***. PMID: 28362261 Huang et al., ***Mol Plant***. PMID: 27756575 Huang et al., ***Cell Host …

phase-separation plant-immunity Postdoc

updated 24 months ago • Shuai

context of cotranscriptional splicing. I've found a paper (Saeki & Svejstrup 2009, Sigurdsson et al. 2010, Close et al. 2012) that mentions that A-rich tracts cause pausing. The first paper does not provide a reference on this

updated 12.2 years ago • polarise

HI I am using the following set of commands on GATK2.1.13 to generate a VCF file echo java -Xmx20g -jar /usr/bin/GenomeAnalysisTK.jar -I B2_with_ReadGroup.ddup.sorted.bam -R human_g1k_v37.fasta -T RealignerTargetCreator -o my.intervals -et NO_ET -K /root/sandbox/saket.kumar_iitb.ac.in.key echo "Realignment Done at date" echo "Starting IndelRealigner at date" …

gatk variant vcf samtools

updated 7.1 years ago • Saket Choudhary

Hi all, I have read Johnson et al. about ComBat and usage but I am unsure about best practices on that. I have an expression matrix (in linear, not log2 or log2ratio...decreases to -301, shifting below the 25 percentile that is -214.5 .. Is that normal? From Johnson et al. I read that data has to be normalized before ComBat ('We assume that the data have been normalized and expression values...…

microarray

updated 11.3 years ago • fbrundu

I have been using `panX` tool for pan-genome analysis (My computer info: Ubuntu 16.04 LTS, 64 bit version). I followed the instructions mentioned in the manual and installed all the dependencies `(mcl, mafft, fastree, raxml, DIAMOND, treetime)`. After that, I ran the test as mentioned in the tool manual and end up with the following error, mv: cannot stat 'GC00000142_aa_aln.fa': No such file…

bash python genome perl

updated 19 months ago • Kumar

percent SSR cutoff to filter out a repeat, and why? Some figures come to mind, like 80% (Wicker et al. 2007) for repeat classification or 35% in the S. bicolor de novo repeat library (Paterson et al. 2009

filter filtering

updated 10.9 years ago • MrGreen

Status of cell@ Regulated (if available/ extractable!) Mesophyll Proline Johanna et al. 2002 Stress Up Mesophyll Glucose Syamore et al. 2009 Pathogen Down Mesophyll Auxin Huygens et al. 2009 Ca++ Signalling Down...Mesophyll Citric acid Purita et al. 2015 Dro…

pubmed query KEGG semantics literature

updated 3.0 years ago • justinhaselbach

to test robustness of each prediction. All [PhylomeDB][1] resources are also accessible through [ETE2: a Python Environment for phylogenetic Tree Exploration][4]. [1]: http://phylomedb.org/ [2]: http://trimal.cgenomics.org/ [3]: http

msa phylogenetics database

updated 22 months ago • Leszek

counts=data, group=group) dge <-calcNormFactors(dge) dge <- estimateDisp(dge) et <- exactTest(dge, pair=c("wt", "res")) write.csv(et$table,"dacomitinib-edgeR.csv") I am analyisng my sample rnaseq data with EdgeR

edgeR rna-seq

updated 2.7 years ago • edus_bioinfo

B, Basal, Normal like, HER2 enriched) Basal subtype can be divided in basal A and basal B. (Kao et al., 2009; Neve et al., 2006) It has been done using expression from MicroArray via Significance Analysis of Microarrays (SAM

cancer tcga

updated 6.4 years ago • ZheFrench

Hello, I know that Berger et al. 2008 found a PSSM of RAX in mouse; does anybody know where can I find it

pssm mouse matrix

updated 13.9 years ago • Anima Mundi

I'm trying to find/use a popular gene finding tool called genBlastG 1.39 ([She et al. 2011][1]), but the [source website][2] seems to be deprecated, giving me 404 errors. It appears to have not been updated for 7 years...still get the 404 error. But it has been cited by recent genomics papers (e.g. [Navarro-Escalante et al. 2021][3], [Tan et al. 2021][4]), so clearly someone is getting it to work…

gene-finding genBlastG

updated 21 months ago • jaredbernard

the last years. For example, we characterized the telomere length regulators HOT1 (Kappei*, Butter* et al., EMBO J 2013) and ZBTB48 (Jahn*, Rane* et al., EMBO Rep 2017) as well as the ALT-specific telomere binding protein ZBTB10 (Bluhm et...screen to study putative telomere-associated proteins from fish to mammals (Kappei*, Scheibe* et al., Nat Commun 2017). In the future, we want to deepen our u…

proteomics RNA-Seq next-gen ChIP-Seq

updated 19 months ago • IMB postdoc programme

the potential interaction among all of these proteins. From literature, I learned that NetVenn (Wang et al 2014 Nucleic Acids Research) and STRING (Franceschini et al 2014, Nucleic Acids Research) are available, but only for human

gene

updated 3.8 years ago • rajaragupathy

I have a tree constructed from a MSA (done with MAFFT) of around 400 protein sequences. I am using ETE3 to compute a tree using the following pipeline: *none-trial01-pmodeltest_soft_ultrafast-phyml_default*. The resulting

sequence alignment tree phylogenic

updated 6.0 years ago • jduc

I am trying to normalize my virus-metagenomics raw counts based on [ROUX et al, 2017][1]: The authors normalize raw counts by contig size. Afterwards, they transform it to RPKM (edgeR) as correction for...I am trying to normalize my virus-metagenomics raw counts based on [ROUX et al, 2017][1]: The authors normalize raw counts by contig size. Afterwards, they transform it to RPKM (edgeR) as corr…

virus normalization metagenomics edgeR RPKM

updated 3.7 years ago • Arsenal

In December 2011, Hunt et al published a strong refutation of the role of rare functional variants in SIAE in autoimmune disease: http://www.nature.com...false association, and could it have been prevented? One of the potential confounds noted by Hunt et al in their study is that, although principal component analysis is effective at identifying population structure coarsely...in rare variant st…

confound rare-variant population GWAS substructure

updated 2.3 years ago • Vincent Laufer

isoform usage, which is implemented by cuffdiff2 (detailed in the supplement of Trapnell et al.), to estimates calculated by eXpress. Before pressing ahead I wanted to make sure that I am not making an egregious error...fragment abundances and adjusted transcript lengths (referred to as gamma and l(t) in Trapnell et al.), respectively? And is it appropriate to back calculate Var[gamma] directly f…

RNA-Seq cufflinks eXpress isoforms

updated 3.3 years ago • sah9b

exp_study = DGEList(counts=rnaseqMatrix, group=conditions) exp_study = calcNormFactors(exp_study) et = exactTest(exp_study, dispersion=0.1) tTags = as.data.frame(topTags(et,n=NULL)) ``` Images in the link: https://www.dropbox.com/sh

EdgeR logFC next-gen R RNA-Seq

updated 2.9 years ago • sayuj.koyyappurath

is a pervasive cause of sequencing errors, directly confounding variant identification'", Stewart et al., Science **361** eaas9824(2018), authors point out that the method of variant analysis proposed by Chen et al. (Reports, 17 February

SNP

updated 6.1 years ago • gdaly9000

have already been aligned and ultraconserved elements have been identified. For example Miller et al. 2007. Is there a website where I can download a list of ultraconserved elements found in two species? Ideally with some...additional information such as genomic location and percentage identity. Thanks in advance. Miller et al . (2007) 28-Way vertebrate alignment and conservation track in the …

ultraconserved elements comparative genomics

updated 8.3 years ago • ddowlin

you help me about the bowtie2 error message below that I don’t understand? I run HiC-Pro (Servant et al., 2015) for our chicken HiChIP data (Mumbach et al., 2016) with 40bp paired-end reads. HiC-Pro is an aligner based on bowtie2. After...KILL) Best, Gary Reference Mumbach MR, Rubin AJ, Flynn RA, Dai C, Khavari PA, Greenleaf WJ, et al. HiChIP: efficient and sensitive analysis of protein-d…

bowtie2 HiC-Pro HiChIP alignment

updated 7.2 years ago • Gary

Hi everyone, I am using miRNA-mRNA interaction information, when I searched TargetScan v7.2. I see that they have mainly 2 types of data: conserved and unconserved. I read their FAQs and see the definition of "conserve", so if I want to investigate the regulatory network, what should I use? I'm still not getting the definition of "conserve". Could somebody please explain this term? I don't have m…

data

updated 6.0 years ago • landscape95

group. Then, mutual information is calculated. This is best visualized from this graphic in Steuer et al. (2006) My question is how to calculate this mutual information value. I have such a contingency matrix, and know how to calculate...mutual information, but Gibbons et al (and Steuer et al too) use an approximation, and I'm unsure of their notation. The MI for a cluster is additive under th…

gene clustering

updated 13.2 years ago • Ted

Hello, everyone! I get into trouble when I install the soft such as breakdancer, Mutsig which were developed by Ding lab. These are all very common used software in sequencing. I think the reason is that my linux is redhat, not ubuntu, would you help me know whether it is this reason? Thanks!

breakdancer

updated 11.6 years ago • Liyf

AND the enrichment score is 1.23 with p-values of 2.8E-2**: clustered terms are DNA-binding region:ETS (7 genes), Ets (7 genes), Domain:PNT(4 genes), ETS(7 genes), SAM PNT(4 genes) **But for another annotation cluster, there are 86 genes BUT

RNA-Seq ChIP-Seq sequencing

updated 2.3 years ago • parksuhong

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...at the cutting edge of cell reprogramming, neurobiology and computational biology (Signaroldi, Laise et al., Nature Communications 2016; Germain et al., Nucleic Aci…

ChIP-Seq RNA-Seq bioinformatician

updated 21 months ago • ivivek_ngs

y[keep,,keep.lib.sizes=FALSE] y <- calcNormFactors(y, method = "TMM") bcv <- 0.2 et <- exactTest(y, dispersion=bcv^2, pair = c("A", "B")) FDR <- p.adjust(et$table$PValue, method="BH") et$table$FDR <- FDR results_EXT <- as.data.frame...et$table) results_EXT_sig_dn <- filter(results_EXT, FDR < 0.05 & …

edgeR

updated 2.1 years ago • bhanu.chandra1

Johnson D S, Mortazavi A, Myers R M, et al. Genome-wide mapping of in vivo protein-DNA interactions.[J]. Science, 2007, 316(5830):1497-502. but I can't download datasets

ChIP-Seq

updated 8.3 years ago • zzz550987425

heatmap.2(data1, col = col.pan, Rowv = TRUE, scale = "none", > : `x' must be a numeric matrix et <- exactTest(dge, pair=c("ctrl", "tr")) etp <- topTags(et, n=2000000) data1 <- as.matrix(etp$table$logFC) heatmap.2(data1, col=col.pan

edgeR Clustering heatmap

updated 7.2 years ago • Sharon

I found some candidate alternatively spliced exons in a paper by [Gardina et al. (2006)][1] that are annotated by so-called "probeset IDs" from the GeneChip Human Exon 1.0 ST array (e.g. "2425850" for a probeset...of the gene COL11A1). There must be a possibility to map the probeset IDs from Gardina et al. to Ensembl Exon IDs (the mapping doesn't necessarily have to be unique) but somehow I can't…

mapping probeset ID exon Human Exon 1.0 ST

updated 7.0 years ago • sevenless

approach by using in query the assemblages and in database of nucleotide databases containing **ETs**, which would be an approach maybe less sensitive but much faster! Only I can't find a database in ET representative of `eukaryotes

repeat Assembly

updated 4.1 years ago • Chvatil

x4))) y<-DGEList(counts=countsvec, group=groupvec, remove.zeros=TRUE) y<-estimateDisp(y) et<-exactTest(y) et$table$PValue

R rna-seq RNA-Seq differential expression edgeR

updated 4.2 years ago • jmor

Nov 2014). - [Robinson et al.][12] Integrative clinical genomics of advanced prostate cancer. *Cell*. 161(5):1215-28 (21 May 2015). - [Ravegnini et al.][13]. Personalized...rearrangement in clinical cancer specimens. *J Mol Diagn*. 16(1):56-67. (Jan 2014) - [Pennington et al.][20] Germline and somatic mutations in homologous recombination genes predict platinum response and survival in ovarian…

N-of-one WGS RNA-Seq next-gen Exome

updated 3.3 years ago • Obi Griffith

terminal nodes/leaves) together if their average distances to the nearest parent clade is < X (ETE2 Python package). This is biologically interesting since some of the gene regulatory DNA motifs may be homologous (paralogues

homology distance collapse Newick orthology

updated 3.3 years ago • a1ultima

I’m working with some data with large BCV (indicated below). I made my design matrix accounting for all the covariates I possibly could with the metadata I had. I applied conservative gene expression thresholding (eg >= 0.75 log(CPM + 1) measured in >= k% of samples as described in the voom guides and various biostars/bioconductor posts) I compared the mean-variance trends t…

filtering differential-expression voom gene

updated 23 months ago • wiscoyogi

I have human gut microbial gene catalogue (Qin et al., 2010), I would like to find phage genes/prophage region genes among. What would be the best practice

metagenomics phage

updated 10.1 years ago • yax

Hello, Can anyone suggest how to detect deep paralog or inparalog in a phylogenetic tree using ETE toolkit ? get_my_evol_events is not good enough to detect deep paralog in deeper nodes. Thanks in advance. Arun

ETEtoolkit python2.7 phylogeny

updated 8.3 years ago • arunprasanna83

Anyone familiar with the gKaKs pipeline (Zhang et al. 2013): Can this pipeline use transcriptomic data to calculate Ka/Ks? I assume it does, but it would be nice to have confirmation

RNA-Seq next-gen gKaKs transcriptome

updated 6.6 years ago • mah123

to add gene predictions from eggNOG/Cogs into my genome figure like in these examples below: ![Orsi et al., 2015][2] and [Ku et al., 2013][3] The annotation output does not have any information regarding the gene start and end locations

genome annotation R

updated 5.9 years ago • mss

were also used to test positive selection. When I tried to do same analysis (multiple copy approach), ETE tool used only one sequence (one gene) from each species although each species has multiple copies in the same ortholog...family. Is there any way to deal with gene duplication event because ETE uses only the first sequence of each species? Codeml in PAML says Seq occurs more than once in …

genome sequence gene

updated 4.6 years ago • Mehmet

dge <- calcNormFactors(dge) dge <- estimateCommonDisp(dge) dge <- estimateTagwiseDisp(dge) et <- exactTest(dge) etp <- topTags(et, n=30) etp$table$logFC = -etp$table$logFC head(etp, n=15) write.csv(etp$table, "edgeR-control

R Bioconductor RNA-Seq

updated 9.2 years ago • aj123

I am not familiar with RNAseq or 16S analysis...I have never done either. I've read papers ( [Li P et al][1], [Evans et al][2], [Li et al][3], and [Risso et al][4]), but I'm uncomfortable just "winging it". So my first question is: does anyone have suggestions

normalization amplicon depth coverage

updated 6.6 years ago • sovrappensiero

do with the existing SNP data in regards to estimating archaic introgression. I know [Sánchez-Quinto et al. (2012)][1] and [Reich et al. (2011)][2] had used f4 statistics (described in depth by Patterson et al. (2012) [here][3] to estimate Neanderthal

snp genome

updated 3.0 years ago • devenvyas

986 results • Page 3 of 20

Recent Votes

Answer: Recommended reliable enrichment tool

Answer: Write maf file (opposite of read.maf)

Answer: CNV Analysis and Visualisation

Answer: Premade RNA-seq pipeline or custom

A: Conversion of Gene Name to Ensemble ID

Answer: MAF tools - changing tumor sample barcode name

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