Categories
Tag: RPKM
Functional alterations and predictive capacity of gut microbiome in type 2 diabetes
Diversity and compositional analyses Regarding clinical differences (Table 1), T2DM individuals (mean 69.6 (± 12.3 sd) years) were significantly (p value < 0.01; Wilcoxon rank-sum test) older than the controls (46.9 (± 17.3 sd) years), showed higher BMI (mean 30.9 (± 7.01 sd) vs. mean 26.3 (± 6.12 sd) than the control…
Solved Here is a set of expression data (reported as RPKM)
Transcribed image text: Here is a set of expression data (reported as RPKM) for two genes taken at three timepoints during an organism’s development. Use it to answer the next set of questions. Calculate the mean-centered expression level for each gene at each timepoint Write your answer for each question…
how to test for differential expression in samples where a global increase in gene expression is expected
As the title suggestions, I’m wondering what the best way to test each gene in a count matrix containing two groups is, where one group is expected to have a global increase in gene expression. I need to use spike-in normalized RPKM data, so from my understanding of DESeq, it…
Genomic evidence that microbial carbon degradation is dominated by iron redox metabolism in thawing permafrost
Tarnocai C, Canadell JG, Schuur EA, Kuhry P, Mazhitova G, Zimov S. Soil organic carbon pools in the northern circumpolar permafrost region. Global Biogeochem Cycles. 2009;23:1–11. Article Google Scholar Hugelius G, Strauss J, Zubrzycki S, Harden JW, Schuur EA, Ping CL, et al. Estimated stocks of circumpolar permafrost carbon with…
Convert FPKM to TPM in R
I’m conducting a meta-analysis over several datasets. I want to combine those datasets and run some machine learning algorithms to predict a target response. Some of those datasets are raw counts, which I can easily convert to TPM with the following code: rpkm <- apply(X = subset(counts_data), MARGIN = 2,…
smartseq2 RPKM data
Hi! I have smartseq2 RPKM data (already analysed with Seurat pipeline) and I want to do trajectory analysis of my cells. Having RPKM data I wondered whether I can use Monocle 3 or can it just be used with UMI data (10x) ? In Monocle2 it seemed to be possible…
Identification of DNA damage response-related genes as biomarkers for castration-resistant prostate cancer
mRNA expressions of DDR-related genes are upregulated in CRPC compared to those in Pca To identify a cluster of upregulated genes in CRPC, we previously conducted directional RNA-seq analysis using clinical samples obtained from localized Pca and CRPC patients21. We used RNA samples obtained from prostate cancer patients by radical…
IGV not showing bigwig track information
IGV not showing bigwig track information 0 Hi there, I’m struggling to view some .bw files in IGV – however when I load .bam files into IGV (the same ones used to create the aforementioned .bw files) I do not encounter this issue. Whether I have fundamentally misunderstood what a…
Most large structural variants in cancer genomes can be detected without long reads
JaBbA v1 outperforms previous CN algorithms We enhanced our previous JaBbA (v0.1; ref. 4) model with several methodological innovations to increase robustness to read depth waviness, improve algorithm convergence and enforce junction balance for allele-specific as well as total CN (Extended Data Fig. 1a–d and Methods). We also rigorously defined…
Textbook knowledge turned on its head: 3-in-1 microorganism discovered
Phylogenomic reconstruction and metabolic potential of 19 Acidobacteriota metagenome assembled genomes (MAGs) recovered in this study. MAGs from this study (bold) that contained dsrAB are highlighted in red. The class is indicated at the left of the phylogenetic tree and family affiliation on the right (according to GTDB taxonomy99). Abbreviations…
BrdU analysis of yeast replication
BrdU analysis of yeast replication 0 Hi all, I would like to ask how people normalise their data of BrdU-IP sequencing? This is a plot of BrdU-IP-seq across a region in chromosome V in yeast. BrdU labels nascent DNA so here I am basically seeing newly replicated DNA as the…
should I use normalized counts or transformed of normalized counts for RNA-seq association analysis?
should I use normalized counts or transformed of normalized counts for RNA-seq association analysis? 1 Hi, I run differential gene expression with DeSeq2. dds <- DESeq(dds) rld <- rlog(dds, blind=False) vsdata <- vst(dds, blind=FALSE) If my goal is to find association between gene expression (RNA-seq ) and methylation, should I…
Paralog transcriptional differentiation in the D. melanogaster-specific gene family Sdic across populations and spermatogenesis stages
Total Sdic mRNA abundance positively correlates with Sdic copy number in testis Evidence for the presumed enhancing effect of gene duplication on the amount of gene product is mixed. Some studies indicated that no such, or a very limited, effect exists19,38,39,40,41, whereas others found a significant increase17,18,22,42,43. A possible explanation…
Normal vs Tumor – Kaplan Meier Survival Analysis
Normal vs Tumor – Kaplan Meier Survival Analysis 0 To perform survival analysis for normal vs tumor cancer sample what kind of rna seq data is to used? => unstranded => stranded_first => stranded_second => tpm_unstrand => fpkm_unstrand => fpkm_uq_unstrand Which of these shoud be used and is there any…
Biological characterization of coronavirus noncanonical transcripts in vitro and in vivo | Virology Journal
Noncanonical coronavirus transcripts were robustly synthesized and could be categorized into seven populations based on differences in sequence elements To determine the amounts and structures of the noncanonical bovine coronavirus (BCoV) transcripts in HRT-18 cells, nanopore direct RNA sequencing was employed. Quantification by read counts revealed that ~ 30% of the total…
From counts or RPKM > PCA > tSNE visualization of PCA
single cell RNAseq: From counts or RPKM > PCA > tSNE visualization of PCA 2 Hello! I am a beginner at RNA seq analysis, I was hoping someone would point me in the direction of how I can take a data set (~50K genes in rows + 200 cells in…
Questions 2-3) Consider the following diagrams
Transcribed image text: Questions 2-3) Consider the following diagrams showing gene expression levels after whole genome gene expression analysis (e.g. RNA Seq). The experiments are in zebrafish, where MBT occurs around 3 hours post fertilization. Each dot represents a specific gene and both axes represent gene expression levels (read counts…
How to get RPKM from count matrix
How to get RPKM from count matrix 0 Hi Biostars, I have a count matrix with mouse gene name and need to get RPKM. I know it is not a good metric but biologists used to it. gtf <- readGFF(“/reference_genome/mm39.ncbiRefSeq.gtf”) gtf_exon <- gtf[gtf$type == “exon”, ] width <- gtf_exon$end -…
Unveiling the biology of defective viral genomes in vitro and in vivo: implications for gene expression and pathogenesis of coronavirus | Virology Journal
The classification, structure, abundance and reproducibility of coronavirus DVGs RNA transcripts other than those encoded by the coronavirus genome are also synthesized during infection [27]. Based on whether they are relevant to transcription regulatory sequence (TRS) (Figure S1A), a sequence motif from which subgenomic mRNAs (sgmRNAs) are synthesized, coronavirus RNA…
ATAC-Seq and RPKM
ATAC-Seq and RPKM 1 Hi, I want to calculate RPKM of ATAC-Seq data but I do not find any script for that. As I am new to bioinformatics, so would be grateful if somebody guide me. RPKM ATAC-Seq and • 216 views The simplest would be to read the matrix…
Calculating TPM from featureCounts output
Calculating TPM from featureCounts output 3 Hi all, Have a simple question but just want to double check I’m not doing something stupid. I have paired-end RNA-seq data for which I have used featureCounts to quantify raw counts. I now want to normalize using the TPM formula. I read this…
Is it possible to convert 3 prime sequencing read counts into TPMs?
Is it possible to convert 3 prime sequencing read counts into TPMs? 1 I have got read counts from 3 prime sequencing and would like to make a rough comparison with other RNAseq dataset for which have got transcripts per million (TPM) values. Is it possible to convert the read…
How To Read Chip-Seq Data
Source: Youtube.com The era of big data has revolutionized the way we analyze and interpret complex biological systems. In the field of genomics, Chip-Seq (Chromatin Immunoprecipitation Sequencing) data has become a valuable resource for understanding gene regulation and the functionality of the genome. Chip-Seq data provides insights into the binding…
Hugo_Symbol to Entrez ID
Hello, I have Myeloid-Acute Myeloid Leukemia (AML) RNAseq data file data_mrna_seq_rpkm.csv. This file has Hugo_Symbols for all 22,844 genes but not its Entrez IDs. I was able use to two methods in R programming 1) library(org.Hs.eg.db) mapIDs method and 2) biomaRT method to get the entrez_ID of only 16,569 genes…
Species-specific responses of marine bacteria to environmental perturbation
Worden AZ, Follows MJ, Giovannoni SJ, Wilken S, Zimmerman AE, Keeling PJ. Rethinking the marine carbon cycle: Factoring in the multifarious lifestyles of microbes. Science. 2015;347:1257594–1257594. PubMed Google Scholar Moran MA. The global ocean microbiome. Science. 2015;350:aac8455–aac8455. PubMed Google Scholar Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K,…
Dryad | Data — Data for: RNA-Seq dataset of RBL-2H3 (RPKM)
README RNA-Seq data for RBL-2H3 cells. [1]Content Introduction: The coverage of each gene, expression of gene(RPKM), total number of reads that aligned to gene, the description of gene are provided in this analysis. [2]format description: RNA-Seq results are presented in xlsx table, named *.Gene.rpkm.xlsx, each independent sample correspond to a…
Systemic epigenome-wide association study of elk treponeme-associated hoof disease
Study samples were obtained from Rocky Mountain elk collected in Washington, Idaho, and South Dakota and from Roosevelt elk from Washington, Oregon, and California. Only cases with required metadata (location of collection and sex) and confirmed diagnosis of TAHD present or not detected were included in the analysis. Treponeme-associated hoof…
Bioconductor – Linnorm
DOI: 10.18129/B9.bioc.Linnorm This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see Linnorm. Linear model and normality based normalization and transformation method (Linnorm) Bioconductor version: 3.16 Linnorm is an algorithm for normalizing and transforming RNA-seq, single cell RNA-seq, ChIP-seq count data or any large…
Is it okay to normalize data once more?
Is it okay to normalize data once more? 0 I am building deep learning classification model for scRNA, currently, but datas that I processed different normalization. My deep learning model use normalize_per_cell in scanpy, but some of datasets have raw expression count data, and some processed RPKM before. Is it…
PanCanAtlas EBPlusPlus-corrected RNA-seq TCGA dataset
PanCanAtlas EBPlusPlus-corrected RNA-seq TCGA dataset 4 Hi, I am wondering in which normalisation format (RPKM, FPKM, TPM,… etc) the PanCanAtlas EBPlusPlus-corrected RNA-seq TCGA dataset (the EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv file available here) is in? I know it is batch-corrected, but I don’t know in which normalisation format the original data was in. Thanks…
Inter-bacterial mutualism promoted by public goods in a system characterized by deterministic temperature variation
Location and sample collection Samples were taken from 10 composting piles (between May and August 2020) at a food waste (FW) composting facility (Zhejiang, China; 30°52′51.50″N; 119°46′12.87″E). A consistent pre-treatment method was used for each pile. Specifically, about 8 tons of FW was collected every 3 days and subsequently crushed into…
Normalisation on subset of genes
Normalisation on subset of genes 0 Hi everyone My lab collected blood plasma cfRNA samples from breast cancer patients and non-cancer patients as controls. The PI designed a custom gene-chip to sequence 65 genes he predicts will be upregulated in cancer patients. He did this to save cost (cheaper than…
Can we use exon- counts to calculate coverage?
Can we use exon- counts to calculate coverage? 0 Hi all, I was wondering if you could help me with this. I currently don’t have access to the bam or fastq files of the samples I’m working on from a public database. But I do have exon counts for these….
TimeTalk uses single-cell RNA-seq datasets to decipher cell-cell communication during early embryo development
Curation of early-embryo development single-cell RNA-seq data sets for studying cell-cell communication To identify and study eLRs, we collected public early embryo development scRNA-seq datasets from the mouse MII-oocyte stage to the late blastocyst stage to ensure that scRNA-seq datasets represented every stage of early embryo development. In addition, to…
Is it valid to do a coverage normalization in addition to applying a spike-in-derived scaling factor?
ChIP-seq visualization: Is it valid to do a coverage normalization in addition to applying a spike-in-derived scaling factor? 0 Let’s say a ChIP-seq sample is scaled in the following way: Calculate the percent spike-in reads in the immunoprecipitate (IP) Calculate the percent spike-in reads in the input Calculate the scaling…
Read data file and produce RPKM in edgeR
This post is in response to a number of emails and posts asking about reading data into edgeR and producing RPKM. Suppose we start with a tab-delimited file counts.txt like this: To read this into edgeR: library(edgeR) Data <- read.delim(“counts.txt”, sep=”\t”, row.names=1) y <- DGEList(Data, annotation=”Length”) To normalize the library…
Extract RPKM values from Diffbind
Extract RPKM values from Diffbind 2 Hi everyone, does anyone know if there is a way to extrapolate rpkm values from Diffbind?? Thanks Francesca ChIP-Seq Diffbind RPKM • 1.1k views You can set the read score to DBA_SCORE_RPKM in dba.count(). You can do this when you originally count, or anytime…
Nitrogen and phosphorous acquisition strategies drive coexistence patterns among archaeal lineages in soil
Nitrososphaeria AOA dominate archaeal and nitrifier assemblage throughout the year Nitrososphaeria AOA represented 79.4–100%, 75.4–98.0%, and 73.4–98.6% of total archaea and 2.8–7.6%, 1.0–1.8%, and 1.2–2.3% of total microbial communities in 16S rRNA gene amplicon, metagenome-recovered 16S rRNA genes, and prokaryotic rpoB-normalized amoA gene reads, respectively, throughout the year (Fig. 1A–C). Non-ammonia-oxidizing…
How to deal with two dataset of RNA expression
How to deal with two dataset of RNA expression 1 Hi all. I am anaylzing two dataset from GEO database. One is data of RNAseq, and under CPM and RPKM processing. Another seems from microarray,which describes the data processing as “The data were analyzed with Microarray Suite GCOS using Affymetrix…
Which zUMIs output to use for differential gene expression?
Which zUMIs output to use for differential gene expression? 0 I have single cell Smart-Seq 3 data. The zUMIs pipeline produces about 19 different output count matrices: umicount exon all downsampled inex all downsampled intron all downsampled readcount exon all downsampled inex all downsampled intron all downsampled readcount_internal exon all…
Boquila: NGS read simulator to eliminate read nucleotide bias in sequence analysis
. 2023 Feb 21;47(2):158-163. doi: 10.55730/1300-0152.2650. eCollection 2023. Affiliations Expand Affiliations 1 Faculty of Engineering and Natural Sciences, Sabancı University, İstanbul, Turkey. 2 TÜBİTAK Research Institute for Fundamental Sciences, Gebze, Turkey. Item in Clipboard Ümit Akköse et al. Turk J Biol. 2023. Show details Display options Display options Format AbstractPubMedPMID ….
Transcriptomic analysis of neutrophil apoptosis induced by large B-cell lymphoma
introduce Difuse large B-cell lymphoma is the most common subtype of non-Hodgkin lymphoma, accounting for 30 percent of new cases in NHL each year. Although approximately 50-60% of human patients are cured by R-CHOP immunochemotherapy, more than 30% of patients are refractory to these regimens or relapse after remission, and…
How to interpret heatmap using plotheatmap from deeptools?
How to interpret heatmap using plotheatmap from deeptools? 1 The heatmap indicates by color the amount of signal (whatever this is, RPKM, TPM, normalized counts…) in a windows of +/- 3000bp around the TSS which is the center. The more blue the more signal, the more red the less signal….
How to best represent three biological replicates of single tissue sample?
How to best represent three biological replicates of single tissue sample? 1 Hello All, Curious as to how to best represent three biological replicates of a single tissue sample of RNASeq data? Assuming that these each replicates are normalized (RPKM, TPM), is there any other statistical analysis that needs to…
Identification of a deep-branching thermophilic clade sheds light on early bacterial evolution
Lieph, R., Veloso, F. A. & Holmes, D. S. Thermophiles like hot T. Trends Microbiol. 14, 423–426 (2006). Article CAS PubMed Google Scholar Hedlund, B. P. et al. Uncultivated thermophiles: current status and spotlight on ‘Aigarchaeota’. Curr. Opin. Microbiol. 25, 136–145 (2015). Article CAS PubMed Google Scholar Kato, S. et…
Crosstalk between KIF1C and PRKAR1A in left atrial myxoma
Two rare variations of KIF1C were identified by WES and RNA-seq Eighteen PBMCs samples and sixteen myxoma tissue samples were included in the research. A flowchart showing the experimental design, sample details, and distribution of variations is shown in Fig. 1a. Sanger sequencing for the exons of PRKAR1A was carried out…
Revisit where to find CCLE RNAseq in FPKM or RPKM using RSEM values to perform normalization- as was never answered usefully
Revisit where to find CCLE RNAseq in FPKM or RPKM using RSEM values to perform normalization- as was never answered usefully 0 I would like to find the CCLE RNA expression file that has either effective gene sizes or FPKM /RPKM (where estimated RSEM values have been used) to do…
the problem with rpkm (and tpm)
Can you please explain the main core problem with RPKM normalization (as a measure of relative abundance), using a simple example, and why TPM solves this? Different explanations for why the RPKM unit is bad are: (a) it uses length normalization, (b) it normalizes to total library size, (c) because…
Threshold for a value of RPKM considered significant
Threshold for a value of RPKM considered significant 1 Hi all, My lab don’t have money to have biological replicates for bulk-RNA seq, so I can’t perform DEG but only get a RPKM table. I found this question being asked but I am not sure if we have any update…
Appropriate RPKM cutoff
Appropriate RPKM cutoff 0 Hey, I’m using multiple previously published RNA-Seq studies as validation and to search for similar “signatures” as in our data. For these other studies I have their final read counts, and statistically significant filtered data that includes RPKM, FPKM, or other normalized read values as per…
Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels
Dubilier N, Bergin C, Lott C. Symbiotic diversity in marine animals: the art of harnessing chemosynthesis. Nat Rev Microbiol. 2008;6:725–40. Article CAS PubMed Google Scholar Sogin EM, Kleiner M, Borowski C, Gruber-Vodicka HR, Dubilier N. Life in the dark: phylogenetic and physiological diversity of chemosynthetic symbioses. Annu Rev Microbiol. 2021;75:695–718….
same peak ID across multiple experimental conditions?
ATAC peak-calling: same peak ID across multiple experimental conditions? 0 I’m trying to reproduce the ATAC analysis here. I have a few questions about alignment and peak-calling. In the “ATAC-seq alignment” section in Method Details, they use Trimmomatic to remove adapters. However, I don’t know the adapter sequence. Would it…
43.6 million passengers carried by Emirates Airlines in a year
v + T – normal size Emirates Airlines carried 43.6 million passengers, a growth of 123%, in the fiscal year 2022/2023, with a seat capacity increase of 78%, and seat occupancy of 79.5%, compared to 58.6% in the previous fiscal year. RPKM increased by 7% to 37.5 fils (10.2 US…
Average bigwig files (not sum)
Average bigwig files (not sum) 1 Hello, I have bigwig (RPKM) files of a chip-seq experiment for treatment and control conditions which I am trying to compare. I have 3 replicates for control and 5 replicates for treatment condition. To show the average difference in signal, I merged the replicates…
Streamlined quantitative analysis of histone modification abundance at nucleosome-scale resolution with siQ-ChIP version 2.0
In this section, we derive a simplified expression for the proportionality constant \(\alpha\) that enables quantitative ChIP-seq and we introduce some consequences for track building. This new expression is more intuitive to understand, easier to evaluate, and more accurate to sequencing outcomes than the previous expression. While values derived from…
Obtaining TPM values from STAR alignment and counts with featurecounts using R’s tidyverse syntax (dplyr and tidyr)
Hello! I have a table of counts that I got by aligning rna seq samples with STAR and using featureCounts, and my goal is to get TPM values for each gene of the table. As a first step, I imported my table into R and modified it a bit to…
RPKM normalization
RPKM normalization 1 I have strand specific RNASeq data. I have mapped sequences of negative strand on Negative strand bam file and positive strand sequences on positive strand bam file. I got the read counts. Now, I have to RPKM normalize it, but I am confused weather I should take…
ChIP-Seq experiment, MACS2 bdgpeakcall 0 fold-change, pvalue and qvalue
Hello, I’m currently following this paper Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. It is a ChIP-Seq to generate genome-wide maps of 34 chromatin modifications (17 acetylation marks, and 17 methylation marks) and the histone variant H2AZ. B cells were either naïve (G0) or activated for…
Metagenome-derived virus-microbe ratios across ecosystems
Abstract It is generally assumed that viruses outnumber cells on Earth by at least tenfold. Virus-to-microbe ratios (VMR) are largely based on counts of fluorescently labelled virus-like particles. However, these exclude intracellular viruses and potentially include false positives (DNA-containing vesicles, gene-transfer agents, unspecifically stained inert particles). Here, we develop a…
Gene Expression Analysis c Flashcards
What is used to measure transcript abundance? a variety of units, which have different requirements in order to ensure comparisons are meaningful number of reads that align to a given feature What unit does differential expression often use? What do counts depend on? sequencing depth/library size and on feature length,…
Hoe calculate RPKM from RUVr?
Hoe calculate RPKM from RUVr? 0 I have an RNA-seq count table which is generated by integrating several studies. I want to calculate RPKM but first I run RUVr to remove the unwanted variables. I want to know if I use normCounts(RUVr) to calculate RPKM, would it be correct? RUV…
Anaerobic thiosulfate oxidation by the Roseobacter group is prevalent in marine biofilms
Novel Roseobacter strains isolated from marine biofilms We isolated and cultured bacterial strains from biofilms on natural rocks immersed in coastal waters. After preliminary analyses of 16S rRNA gene sequences generated by Sanger sequencing, more than 500 non-redundant strains were identified, including 54 distant strains affiliated with Roseobacter (hereafter referred…
How to normalise ChIP-Seq samples using deeptools
How to normalise ChIP-Seq samples using deeptools 0 I was wondering what is the best approach to normalising Chip-seq samples using the deeptools software. In our data set we’re using an antibody to pull down specific regions of the genome. But when I do the coverage plot I already get…
New research shows that bacteria get ‘hangry’ too
Microfluidic probe-based scRNA-seq method and validation. a, Cells were fixed and permeabilized to allow the penetration of thousands of unique, genome-specific oligonucleotide probes. Hybridized probes retrofitted transcripts with a poly-A tail and UMI, whereas unhybridized probes were washed away. b, Permeabilized cells with hybridized probes were flowed through a commercial…
How to “guess” the transformation based on already-transformed, “normalized count data”?
How to “guess” the transformation based on already-transformed, “normalized count data”? 2 Thanks for your attention, TLDR: The minimum value in a transformed count matrix is -2.57. How can I guess what transformation was applied? Any good advice on performing differential gene analysis on such transformed data? Details: I would…
Question about mixing TPMs/RPKMs in deconvolution analysis
Question about mixing TPMs/RPKMs in deconvolution analysis 0 Hi all, I have a rather silly question that I’m fairly certain I know the answer to, but since I have never performed cellular deconvolution myself, nor do I have experience in typical workflows for the analysis/using the tools needed, I’ll ask…
Multi-faceted metagenomic analysis of spacecraft associated surfaces reveal planetary protection relevant microbial composition
. 2023 Mar 22;18(3):e0282428. doi: 10.1371/journal.pone.0282428. eCollection 2023. Sarah K Highlander 1 , Jason M Wood 2 , John D Gillece 1 3 , Megan Folkerts 1 , Viacheslav Fofanov 3 4 , Tara Furstenau 3 , Nitin K Singh 2 , Lisa Guan 2 , Arman Seuylemezian 2 , James N Benardini 2 , David M Engelthaler …
Fighting rare cancers: lessons from fibrolamellar hepatocellular carcinoma
I was trained in cell biology and biophysics and, as I was often reminded by study section reviewers, I am “not a cancer biologist”. My closest collaborator, the cell biologist Gunter Blobel6, with whom I had worked for 25 years, encouraged me to leap off in this new direction, building upon…
Calculate RPKM
Calculate RPKM 0 Hi bioinformaticians, would anyone calculate RPKM from the count matrix with edgeR or DESeq2? I found some resources guide on this but there are one or two steps I don’t know such as this: y <- DGEList(counts=counts,genes=data.frame(Length=GeneLength)) y <- calcNormFactors(y) RPKM <- rpkm(y) How to get GeneLength?…
Calculating RPKM for DESeq
Calculating RPKM for DESeq 1 Hi friends DESeq works via count table and create DE genes by count fold change, but it’s better to know about gene RPKM values. Is there any possible way to use / show RPKM for DESeq’s output? And how can i normalized those RPKM values?…
Hypoxia-induced transcriptional differences in African and Asian versus European diabetic cybrids
Human subjects Research involving human subjects was approved by the Institutional Review Board of the University of California, Irvine (#2003-3131). All enrolled patients provided written, informed consent. Clinical investigations were performed based on the ethical principles of the Declaration of Helsinki26. Cybrid generation Patient blood was collected in tubes containing…
A gene silencing screen uncovers diverse tools for targeted gene repression in Arabidopsis
A gain-of-function screen for regulators of gene silencing We utilized the native Arabidopsis gene FWA as a reporter to screen for regulators of gene silencing. FWA encodes a transcription factor that causes a late flowering phenotype when overexpressed, resulting in a greater number of leaves produced before flowering. In Col-0…
Solved 2) Consider the following comparisons corresponding
Transcribed image text: 2) Consider the following comparisons corresponding to genes ( 3 pts) Consider the following experimental comparisons (in all cases Y axis vs X axis in that order) in experiments to detect transcript levels (RPKM or counts for each gene, using RNA Seq) for specific zygotic-only products WT…
Transcription of MERVL retrotransposons is required for preimplantation embryo development
MERVL exhibits distinct localization in mouse embryos To understand the dynamics of MERVL expression, we first analyzed publicly available single-cell RNA-sequencing (scRNA-seq) datasets from each blastomere at eight representative stages of preimplantation development18 (Fig. 1a). To define regions of nonredundant MERVLs in mouse genome, we used RepeatMasker to annotate the…
Rating: Hold; SpiceJet plans long-term expansion strategy
By Nuvama research SpiceJet’s (SJ) reported a positive EBITDAR of Rs 5.9bn as demand increased during the festive season. The return of aircraft and a waiver on lease rental also contributed to the growth of EBITDAR. Highlights: SJ’s lack of transparency in sharing its key operational data (RPKM, CASK) since…
Get TPM from RNA counts and gene length?
Get TPM from RNA counts and gene length? 1 Hello, I am working with an RNA-seq FeatureCounts output file that supplies the counts for a given ENSG gene ID, as well as the gene length(according to documentation this is in base pairs, not kilobases). Is there a way to obtain…
Normalization for RNAseq data – JMP User Community
The JMP Genomics has a few normalization methods for RNAseq data, including KDMM, RPM scaling, TMM, TPM and upper quartile scaling. The JMP Pro 17 is missing such important tools. The purpose of normalization methods for RNAseq or other large scale data, such as metabolomics, is to reduce systematic experimental bias…
A molecular atlas reveals the tri-sectional spinning mechanism of spider dragline silk
Chromosomal-scale genome assembly and full spidroin gene set of T. clavata To explore dragline silk production in T. clavata, we sought to assemble a high-quality genome of this species. Thus, we first performed a cytogenetic analysis of T. clavata captured from the wild in Dali City, Yunnan Province, China, and…
3Q results reflect strong demand and pricing
Revenue grew 61% YoY on 34% volume growth. Yield (revenue/RPKM) increased 22% YoY and 6% QoQ to Rs5.38. Ebitdar margin improved 21ppt QoQ and 80bp YoY to 21.3% (250bp beat). If we exclude the MTM hit on Forex liabilities, Ebitdar margin came in at 25.3%, a 14-quarter high. Absolute Ebitdar…
World First Study Sheds Light On Why Microbes In The Deep Ocean Live Without Sunlight
The abundance of metabolic marker genes is shown on the basis of the metagenomic short reads across the seawater sampled from the three study sites (left; n = 14), metagenomic short reads from the Tara Oceans dataset (middle; n = 213; replicates averaged) and metatranscriptomic short reads from the Tara Oceans dataset (right; n = 89;…
How to choose Normalization methods (TPM/RPKM/FPKM) for mRNA expression
How to choose Normalization methods (TPM/RPKM/FPKM) for mRNA expression Why do mRNA expression values need to be normalized? The unification of mRNA expression value measurements across studies, or the normalization of mRNA data, is a significant problem in biomedical and life science research. The abundance of transcripts is measured digitally…
High fuel prices, depreciation of rupee to hamper margins in aviation sector
Even as the recovery in the aviation sector has been highly impressive with stable traffic at around 90 per cent of pre-Covid levels, Brokerage firm Prabhdas Lilladhar has said the domestic passenger traffic is likely to decline nearly 8-9 per cent QoQ, led by the seasonal nature of Indian aviation…
Bedtools Bam To Bed With Code Examples
Bedtools Bam To Bed With Code Examples With this article, we’ll look at some examples of how to address the Bedtools Bam To Bed problem . bedtools bamtobed [OPTIONS] -i <BAM> As we have seen, a large number of examples were utilised in order to solve the Bedtools Bam To…
TPM and RPKM normalization from counts dataframe
TPM and RPKM normalization from counts dataframe 2 Folks: I have two dataframes for counts information from two RNAseq data… is there a quick way to get from counts to TPM or RPKM or both efficiently? Thanks RNA-Seq • 3.5k views • link updated 5.8 years ago by Ron ★…
TPM normalization starting with read counts
Hello everyone I have multiple bulk RNA-seq datasets that I need to apply the same pipe line on. I want to normalize them from counts data to TPM. In all datasets, I have the genes as rows, and samples as columns. Unfortunately, I don’t have the fastq files, all I…
longer object length is not a multiple of shorter object length
Warning – longer object length is not a multiple of shorter object length 0 I have a counts dataframe of RNA-seq dataset, and got the gene lengths using this code: exons = exonsBy(EnsDb.Hsapiens.v86, by=”gene”) exons = reduce(exons) len = sum(width(exons)) INDEX = intersect(rownames(counts),names(len)) geneLengths = len[INDEX ] counts = counts[INDEX…
Merge multiple text files to create a combined dataframe and rename columns in R – General
Hi, I have multiple .txt files (each file contains 4 columns; an identifier Gene column, a raw_counts and other columns). I would like to merge those files into a combined dataframe using the common gene column. I was able to import multiple .txt files together, merge based on identifier column,…
Metagenomics – RPKM calculation
Normalization for comparing gene coverage values. RPKM corrects differences in both: sample sequencing depth and gene length. RPKM – Reads per kilo base per million mapped reads Formula RPKM = numReads / ( geneLength/1000 * totalNumReads/1,000,000 ) numReads – number of reads mapped to a gene sequence geneLength – length…
a strange pattern of repetitive summits
Problem with the output of Deeptools PlotProfile: a strange pattern of repetitive summits 0 Hi! I am trying to plot DNA binding profiles of my ChIP-seq bw files using Deeptools plotProfile. I generated the matrix using the computeMatrix reference-point. I used some publicly available bed files as my regions of…
RPKM threshold estimation – SEQanswers
Dear All, I have a doubt in the calculation of False postitive rate while checking for FPKM threshold in a RNAseq experiment. Following the method previously published (www.ploscompbiol.org/article/…l.pcbi.1000598). I am not getting desired results. I followed the method as mentioned the publication Reads were mapped to Ensembl genes (blue) and…
RPKM, how to normalize for library size
RPKM, how to normalize for library size 1 Hi everybody! I’m working on several metagenomes (so not trascriptomes), and I mapped high quality reads to a database made of nucleotide sequences through bowtie2. I want to convert raw mapping counts of each gene in RPKM. I know this method might…
Transcriptional profiling of macrophages reveals distinct parasite stage-driven signatures during early infection by Leishmania donovani
Infection with L. donovani amastigotes or promastigotes promotes early changes in the mRNA pool of the host cell To compare the early effects of the two life stages L. donovani in the mature mRNA pool of the host cell, total cytosolic mRNA extracts from bone marrow-derived macrophage (BMDM) cultures infected…
Can I convert HTSeq count into RPKM or TPM value or standard unit of RNA-Seq
Can I convert HTSeq count into RPKM or TPM value or standard unit of RNA-Seq 0 Now, I’m comparing RNA expressions that have RNA-Seq and HTSeq count How can I interpret it together with different unit or Can I convert HTSeq count equivalent RNA-Seq? or if you have other suggestions,…
use tcgabiolinks package to download TCGA data
TCGA Data download in terms of ease of use ,RTCGA The bag should be better , And because it’s already downloaded data , The use is relatively stable . But also because of the downloaded data , There is no guarantee that the data is new .TCGAbiolinks The package is…
How to do functional analysis on differentially expressed gene list from RNA-seq data?
How to do functional analysis on differentially expressed gene list from RNA-seq data? 0 @06f08eeb Last seen 1 day ago Canada Hi all, I am a complete beginner in terms of bioinformatics analysis and I am hoping to complete some functional analysis on some differentially expressed gene lists of some…
DESeq2 input from GDAC firehose
Hi guys, I hope you are fine. I’m not good in English so if you couldn’t understand my question, please feel free to reply. I’m a beginner of bioinformatics. I want to practice differential expressed gene (DEG) analysis in R. The RNA seq data I used was downloaded from broad…
How to perform deconvolution with RPKM values
Hi Xuran, I tried to apply MuSiC to RNAseq bulk data with RPKM as the input. According to your paper(Discussion), “MuSiC can utilize RPKM if estimates of cell type-specific total RNA abundance can be provided.” I am wondering how I can incorporate cell-type-specific total RNA abundance into your function? Or…
r – RNA-Seq Data Heatmap: Is it necessary to do a log2 transformation of RPKM values before doing the Z-score standardisation?
I am making a heatmap using RNA-Seq data in R. The heatmap shows gene expression values (RPKM) in different brain regions. I have the following code: library(tidyverse) library(pheatmap) library(matrixStats) read_csv(“prenatal_heatmap_data.csv”) -> all_data all_data %>% column_to_rownames(“Brain Region”) -> heatmap_data heatmap_data %>% pheatmap() Which generates the following heatmap: I want to do…
New bioinformatics method to analyze viral sgRNA
Single guide ribonucleic acid (sgRNA) molecules are produced by discontinuous transcription, in which viral RNA-dependant RNA polymerase pauses early negative-sense RNA synthesis and then jumps to the other end of the genome. The specifics of this process are still not fully understood. Since sgRNAs can play an important role in…
New bioinformatics method for viral sgRNA analysis
Single guide ribonucleic acid (sgRNA) molecules are produced by discontinuous transcription, in which viral RNA-dependant RNA polymerase pauses early negative-sense RNA synthesis and then jumps to the other end of the genome. The specifics of this process are still not fully understood. Since sgRNAs can play an important role in…