Biostar

986 results • Page 4 of 20

into problems with Genemark. Braker runs till it gets to the stage: NEXT STEP: execute GeneMark-ET. It then produces this error failed to execute: perl /path/to/braker/BRAKER/gm_et_linux_64/gmes_petap/gmes_petap.pl --sequence...path/to/braker/BRAKER/braker/guava/genome.fa --ET=/path/to/braker/BRAKER/braker/guava/hintsfile.gff --cores=8 --soft 1000 1>/scratch/sysusers/godwin/BRAKER/Br…

Assembly

updated 8.5 years ago • mafireyi

Hi, I need to install GeneMark-ES/ET/EP in one of my conda environments and I was wondering how to to this. I would normally do "conda install .... " but this would not...Hi, I need to install GeneMark-ES/ET/EP in one of my conda environments and I was wondering how to to this. I would normally do "conda install .... " but this would not work

conda bioconda

updated 9 months ago • Diego

anyone know of an RNAseq dataset with a large number (min 5-10) of replicate - like the [Bottomly et al 2011 dataset][1] but with paired-end reads? Cheers Kristoffer [1]: https://www.ncbi.nlm.nih.gov//pubmed/21455293

RNA-Seq dataset

updated 6.7 years ago • kristoffer.vittingseerup

as branch label. Can anyone suggest a tool available ? ofcourse not with paint ! Is it possible in ETE toolkit ? Thanks, AP

phylogeny tree annotation ETE

updated 7.0 years ago • arunprasanna83

The RMA paper by Irizarry et al. (2002) specifies how probe sets are summarised (background-correction, quantile normalisation, fit a linear model). I would

exon array affymetrix

updated 12.4 years ago • polarise

I m a beginner in programming, and I was asked to process some fastq files downloaded from casement et al 2018. I found that I need to trim the reads as a start and continue processing the files afterwards. I am not sure how to do

R fastq processing

updated 4.4 years ago • bousbiat.ilhem

programming language) code for Network Component Analysis, proposed in the following paper: Liao et al., (2003) "Network component analysis: Reconstruction of regulatory signals in biological systems", PNAS, 100 (26) I came across...Page not found" Network Component Analysis has been used in many other papers (for example: Ling et al., (2013) "Transcriptome response to alkane biofuels in Saccha…

matlab nca python network-component-analysis

updated 15 months ago • sayakm.biotech

group<-c(1,1,2,3) y <- DGEList(counts=x, group=group) y <- estimateDisp(y) et <- exactTest(y,pair=c(1:2) topTags(et) [1]: /media/images/2029caf8-dc3f-4f52-ae89-2d0b660f

RNASeq edgeR

updated 2.7 years ago • veronica

been reading some papers about Enhancer-Promoter Interactions Prediction such as: - Roy, Sushmita, et al. "A predictive modeling approach for cell line-specific long-range regulatory interactions." Nucleic acids research...43.18 (2015): 8694-8712. - He, Bing, et al. "Global view of enhancer–promoter interactome in human cells." Proceedings of the National Academy of Sciences 111.21

Enhancer Promoter Interactions Prediction Gene

updated 8.5 years ago • Sama

Hello everyone, I need to get the list of gene signatures defined from Bailey et al. and used for tumor subtyping, published in the study: *Bailey P, Chang DK, Nones K, et al. Genomic analyses identify molecular

bailey genes subtype pancreas

updated 4.0 years ago • sabin

a few papers that don't specifically mention this step for microbial RNAseq experiments (i.e. [Yung et al 2016][1], [Tan et al 2015][2]), and other posts that suggest specific rRNA removal is not needed (i.e. [this][3], but for mouse, not microbes

rrna rnaseq ecoli transcriptomics

updated 8.2 years ago • Lina F

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…

next-gen RNA-Seq ChIP-Seq

updated 19 months ago • yang4414

tcga cancer-genomics

updated 20 months ago • yang4414

next-gen genomics postdoc

updated 2.1 years ago • yang4414

Where can I get the genotype calls for the Schuster et al Khoisan and Bantu genomes paper? There's a dataset on the public Galaxy site, specifically "All SNPs in personal genomes

genotyping snp

updated 13.4 years ago • pufferfish

I need to retrieve the list of TCGA glioblastoma samples that were classified as G-CIMP (Noushmehr et al., 2010). In the paper they are not listed (or I wasn't able to find any information about them). Does anybody know where to find

tcga glioblastoma

updated 5.1 years ago • Chip

how to build input files for tissue-based expression data for the DEPICT tool (PMID: 25597830; Pers et al. Nat Commun. 2015, 6:5890)? Any help would be appreciated. Thanks

genetics gene prioritization

updated 4.1 years ago • unepanthere056

spanning regions, number of non-polar helices, whether the protein is functional or structural, et cetera

protein database membrane

updated 10.2 years ago • Good Gravy

not design the events specific primers. The primers span the events. Reference: [1] Brosseau, J. P., et al. (2010). "High-throughput quantification of splicing isoforms." RNA 16(2): 442-449. [2] Tokheim, C., et al. (2014). "PrimerSeq: Design and

alternative-splicing primer-design RNA-Seq

updated 24 months ago • pengchy

Vesicles from Porcine Adipose Tissue-Derived Mesenchymal Stem Cells" In the article cited, Erin et al. claim to have “comprehensively characterized the mRNA and miRNA expression profile of EVs derived from porcine adipose...analysis, CAP-miRSeq and mirDeep2, were designed specifically for small RNA-Seq libraries. Erin et al. do not mention anywhere in their article any adaptation they brought to…

next-gen RNA-Seq

updated 21 months ago • ablanchetcohen

as Ingrid Felicidade, Egon Willighagen, Friederike Ehrhart, Kristina Hanspers, Martina Kutmon, et al. But not the study https://www.wikipathways.org/instance/WP3599

wikipathways

updated 3.5 years ago • salman_96

multiple QPCR. But in the actural transcriptome analysis process, there are no ck genes, like actin et al. So I want to know how can we confirm the different treatments have a same comparison background? Many thanks in advance

RNA-Seq

updated 2.8 years ago • 2012201024

Hi, Does anyone have any experience with kSNP (Gardner et al, 2010)? It was referred by some colleagues while at a meeting. I am told it is difficult to install (I am finding this true) but

updated 12.5 years ago • joe.loquasto

found such a text: 2.1 Training dataset The training dataset contains data from ePSORTdb 2.0 (Rey et al., 2005b), which was used to build PSORTb 2.0, Swiss-Prot version 49 (Wu et al., 2006), plus protein localization data obtained from

uniprot

updated 11.5 years ago • Marcinmagnus

subtype classifications such as Bailey, Collisson and Moffitt. > Bailey, P., Chang, D., Nones, K. et al. Genomic analyses identify molecular subtypes of pancreatic cancer. Nature 531, 47–52 (2016). https://doi.org/10.1038/nature16965...gt; Collisson, E., Sadanandam, A., Olson, P. et al. Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy. Nat Med 17, 500–…

RNA-Seq

updated 4.2 years ago • jack.henry

target** In pursuit of new tumor immunotherapy targets for triple negative breast cancer (TNBC), Ji et al. applied Novogene’s bulk RNA-seq and scRNA-seq strategy to identify Lgals2, gene encoding galectin-2, as a potential target...1] Following in vivo CRISPR screens targeting disease-related immune genes in TNBC mouse models, Ji et al. employed transcriptomic analysis to identify candidate gene…

immunotherapy therapeutic-targets drug-development rnaseq single-cell-sequencing

updated 14 months ago • Novogene

The 1000 Genomes Selection Browser is a database of Signatures of Selection in the Human Genome, based on the 1000 Genomes Phase I data. It is freely accessible at http://hsb.upf.edu/ The browser, based on a custom UCSC Genome Browser installment, allows to easily navigate the genome and visualize regions that are candidate for having been involved in an event of selection in any of the African…

1000genomes human selection

updated 22 months ago • Giovanni M Dall'Olio

By 'full' I mean that, for example, the rRNA loci would be from the pre-rRNA transcript including ETS/ITS. Bonus points if promoters/terminators are also annotated. Thanks

gtf Annotation gff bed

updated 5 months ago • noodle

format: Est1000HGDP.bed Est1000HGDP.bim Est1000HGDP.fam I have other data from the study by Henn et al. 2012 in the same format: Henn.bed Henn.bim Henn.fam And I want to merge these files with each other, and unfortunately

Plink

updated 3.4 years ago • Max

or even list for common CNVs in humans, I found [one database][1] published by Donald F. Conrad et al in Nature 2010. I would like to ask if you know other useful sources ! Best regards Kiz [1]: https://www.dropbox.com/s/tg3tqf542fbcz61

database cnv gene

updated 3.0 years ago • Kizuna

data by using samtools. Now I need to know where the SNP located(5'-UTR, exon, intron, 3'UTR, et al). So is there any softwere I can use to build a index between genome and annotated mRNA so that I can calculate the variation

index genome mrna snp variant

updated 13.6 years ago • Haiping

of Watson-Crick Base pairs on Termini of Single DNA Molecules" (by Winters-Hilt, Vercoutere, et. al) I'm perplexed by the left side with A,B,C,D,E... - how does it relate the to the FSA on the right? full image: http://i.imgur.com/cgwD6.png

analysis graphs

updated 13.3 years ago • Adel

like to use `match` and `cbind` functions for this. Thank you your help. `df1` ``` Sample MPK ET TRN ATF 44 55 5 CBD 49 22 66 GGY 50 4 77 ``` `df2` ``` Project Sample Target PL-gen ATF 3435 TT-gen TT 22333 HY-gen GGY 43333 ``` Result: ``` Sample...MPK ET TRN P…

cbind dataframe match

updated 2.6 years ago • MAPK

Dear all, I'd like to call nucleosomes from yeast MNase-seq data. In particular, I'm interested in using the PING (Zhang et al., 2012) bioconductor package. The PING documentation discusses all of the post-mapping analysis steps. My question is, however...call nucleosomes from yeast MNase-seq data. In particular, I'm interested in using the PING (Zhang et al., 2012) bioconductor package. The PIN…

ChIP-Seq PING Nucleosome MNase-Seq

updated 8.8 years ago • devking

SNPs: should I subtract them from the superset before performing the test? Thanks! (1) Maurano et al., 2012: https://www.ncbi.nlm.nih.gov/pubmed/22955828 (2) Andersson et al., 2014: https://www.ncbi.nlm.nih.gov/pubmed/24670763

enrichment gwas fisher

updated 8.3 years ago • enricoferrero

I’m reading a paper (CIBERSORT, by Aaron Newman et al, 2015) and the authors mention that all data are “in non-log-linear space.” Authors also mention adding “non-log-linear noise

Data

updated 3.6 years ago • willy

I have <34 VCF files for the 9.9Mb callable NRY bases per Poznik et al. 2013 (10.1126/science.1237619). (One individual per VCF, some are from women, so they will be omitted) I want to construct...I have <34 VCF files for the 9.9Mb callable NRY bases per Poznik et al. 2013 (10.1126/science.1237619). (One individual per VCF, some are from women, so they will be omitted) I want to c…

vcf phylogeny

updated 5.7 years ago • devenvyas

The MISA microsatellite finder (Thiel et al., 2003) is a tool for finding microsatellites in nucleotide sequences. In addition to the detection of perfect microsatellites

RNA-Seq

updated 5.5 years ago • talib429

I've been reading some of the influenza literature (Rambaut, A. et al. The genomic and epidemiological dynamics of human influenza A virus. Nature 453, 615–619 (2008).), and found that these authors

plot

updated 11.6 years ago • ericmajinglong

Hello, dear friends, I am very interesting about the figures [5-8] ploted in paper of D Ruano et. al, which is also displayed in other papers. While I am not very familiar with this kind of analysis, could anyone tell me how

gwas association

updated 10.4 years ago • J.F.Jiang

to a publication where they used pair-end sequencing for a chip-seq experiment? I know about Wang et al. (doi:10.1186/1471-2105-11-81) paper in BMC bioinformatics, but was searching for something done on an animal system. Best

chip-seq paired data

updated 13.5 years ago • Frenkiboy

SNP6 are used for benchmarking the copy-number calling algorithms in the [CNVkit paper][1] (Talevich et al 2015) and the [recent PureCN paper][2] (Oh et al 2020), respectively. Thanks! [1]: https://journals.plos.org/ploscompbiol/article

CNV CGH SNP6 Copy Number NGS

updated 4.7 years ago • robert.mclaughlin

**The Niehrs laboratory** studies regulation of DNA methylation, which plays important roles in development & disease. We have recently demonstrated a role for long non-coding RNAs and R-loop DNA:RNA hybrids in DNA methylation (Arab et al. 2014; Arab et al. 2019). In an ERC-funded project, we now aim to elucidate the mechanisms of DNA demethylation as well as the role played by long non-…

ncRNAs Omics molecular-bio R-loops Postdoc

updated 3.1 years ago • IMB postdoc programme

Hi! I'm testing detection and abundance of viruses in metagenomics (viromics). In ([Roux et al, 2017][1]), The authors state the use of [nucmer][2] (from [mummer][3]) to cluster the contigs: > ' Contigs from all samples were clustered...Delcher, Salzberg & Phillippy, 2003) at ≥95% ANI across ≥80% of their lengths, as in (Brum et al., 2015; Gregory et al., 2016), to generate a pool…

assembly clustering metagenomics virus nucmer

updated 3.9 years ago • Arsenal

reference paper: Decapping of Long Noncoding RNAs Regulates Inducible Genes - Sarah Geisler et al Any help in this regard is really appreciated. Thank you. Ketaki

rnaseq

updated 11.3 years ago • k2bhide

mapping metrics such as mapping rate, unique mapping rate, concordant mapping rate, unmapping rate et al. Is there any way to get this kind of information? Many thanks, Tom

BWA

updated 5.8 years ago • wangdp123

I have computed the microsyntenic regions for my gene family described in many articles eg: [Jin et al. 2016][1], [Chen et al. 2015][2]. I have the data generated like Region Syntenic genes POPTR_0001s10490 - POPTR_0003s13840 POPTR_0001s10340...With this data I could like to create microsyntenic map similar to Figure3 presented in [Jin et …

microsynteny software visualization

updated 8.7 years ago • vharshavardhanan

QUIVER as mentioned in the Genome Assembly with Falcon in the Methods Section of the paper Paajanen et al., Scientific Data, 4:170149, 2017. In the subsection titled "Genome assembly with FALCON" in the Methods Section, the genome...by fc_unzip or ii) running fc_run followed by the quiver based polishing as described by Paajanen et al. ? Also I installed smrtlinks-ttols using conda but this se…

sequencing rna-seq PacBio Quiver FALCON

updated 6.1 years ago • ambarishnag

using the free software R and the R packages ‘metafor’ (Viechtbauer 2010) and ‘orchaRd’ (Nakagawa et al. 2023). The course will follow the principles of open science, with a strong focus on the importance of adhering to preferred...reporting items for systematic reviews and meta-analyses (PRISMA EcoEvo; O’Dea et al. 2021). Throughout, we will consider examples of how to interpret results and pres…

Meta-analysis Review Evidence-Synthesis

updated 8 weeks ago • carlopecoraro2

software tool which will allow me to use the directionality index to call TADs as defined by [Dixon et al. 2012][1]. I found a tool called [Domain caller][2] which I believe has been created by the authors of the paper, however [Rao et al

R next-gen

updated 4.7 years ago • h.long

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Best Practices for ATACseq for Performing Differential Accessibility Analysis

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Number of mapped reads from BAM file

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