Tag: FPKM

Introduction Single-cell RNA sequencing (RNA-seq) was first achieved by using a quantitative cDNA amplification method and applied to mouse oocytes (Kurimoto et al, 2006; Tang et al, 2009). It has since provided unprecedented opportunities for the study of cellular differentiations, states, and diseases in various biological fields, including developmental biology,…

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…

DOI: 10.18129/B9.bioc.zFPKM   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see zFPKM. A suite of functions to facilitate zFPKM transformations Bioconductor version: 3.16 Perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013…

Department of Biotechnology, College of Science, Taif University, Taif, 21944, Saudi Arabia Correspondence: Sarah Albogami, Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia, Email [email protected] Purpose: According to the World Health Organization, Saudi Arabia ranks seventh worldwide in the number of patients with…

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…

A Ct strain severely inhibits plant growth in a nutrient-dependent manner A Ct strain, Ct61, isolated from a wild A. thaliana population in Spain, promotes plant growth under low Pi conditions by transferring phosphorus to the host3. In addition to Ct61, five different Ct strains have been isolated from various…

The real effect of CPSF3 on circRNA expression in HCC cells was tested by analyzing the total RNA fractions obtained from CPSF3-KO HepG2 cells, CPSF3-OE Bel7404 cells, and negative control cells using high-throughput sequencing (Supplementary Files S7 and S8). The data obtained showed that CPSF3-KO cells had more types and…

RGCs from human iPSCs for genomic analysis We developed neuronal organoids, including RGCs from human iPSCs, to assess the effects of low-dose irradiation. Phase-contrast microscopy (Supple Fig. S1a) indicated time-dependent morphological changes in the embryonal body formed from human iPSCs, which corresponded to previous reports14, 15. Retinal development was evaluated…

Clustering is a data mining method to identify unknown possible groups of items solely based on intrinsic features and no external variables. Basically, clustering includes four steps: 1) Data preparation and Feature selection, 2) Dissimilarity matrix calculation, 3) applying clustering algorithms, 4) Assessing cluster assignment I use an RNA-seq dataset…

Calculating FPKM and TPM by hand from htseq-count output? 0 Hello! I am counting reads with htseq-count, and wasted some hours trying to find an extant software that would calculate FPKM and/or TPM from that output, so I wrote a script myself. There is just one question mark – should…

Collecting columns from multiple files into one file 1 Dear all, I hope you are all doing well. I’m new to bioinformatics and would be grateful if you could help me with the below issue. I have 156 files named with sample_1_TEcounts.tsv, sample_2_TEcounts.tsv, … and contain information as in the…

Sample collection, library construction and sequencing Leaves of two diploid C. paliurus (PG-dip and PA-dip) and one auto-tetraploid (PA-tetra) for genome sequencing were collected from plants grown in germplasm bank of C. paliurus, which located in Baima experimental field, Nanjing, Jiangsu province, China. After collecting, tissues were immediately frozen in…

C1A protease family genes in the pineapple MD2 v2 genome Presence of either the C1 peptidase or I29 inhibitor domains were used as a signature to identify genes belonging to the C1A protease gene family9. 71 C1A genes were identified (AcC1A1–AcC1A71), and were distributed across 17 pineapple chromosomes (Fig. 1,…

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…

RNAseq comparing wt strain PcPCL1606 and the derivative mutant AdarB, defective in HPR production. RNA was extracted from the rhizosphere samples using a PowerSoil® RNA extraction kit (Qiagen Iberia S.L., Madrid, Spain) following the manufacturer’s instructions and its amount was quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham,…

Plotting ATAC-seq data over RNA-seq? 0 Hi everyone, I am new to this space and have no bioinformatics background — with very limited knowledge on data processing. So I apologize ahead of time if any of my questions are extremely stupid or make no sense 🙂 I did manage to…

cBioPortal data with negative log2(FPKM + 1) values 0 Hello, I am looking at data downloaded from cBioPortal directly. The metadata for the mrna-seq files asserts the data are log2(FPKM + 1), but there values as small as -0.3 in the matrix. I am thinking maybe they did log2(FPKM) +…

Characterization of genomic landscape We compared somatic variants, copy number alterations, and mutational burden between the primary and metastatic tumors of the ST and LT survival groups. Our cohort of patient tumors exhibited characteristics typical of those seen in previously sequenced HGSC tumors, such as nearly ubiquitous TP53 mutations, high…

Hello, I have a fairly simple question that I know has been addressed many times: I want to import RSEM data into DESeq2 for modeling and DE. For reproducibility, the workflow is: Unfortunately, it is costing me an inordinate amount of time, and I cannot find a perfectly analogous example…

Introduction Skin cutaneous melanoma (SKCM) is the most severe dermatologic malignancy, and its incidence has increased worldwide in recent years.1 SKCM accounts for 1% of all skin cancer patients, yet it is responsible for roughly 80% of all skin cancer deaths.2 Early-stage SKCM (localized or regional) can be surgically removed,…

Timecourse of Hox gene activation in stembryos In gastrulating mouse embryos, Wnt signaling contributes to the formation of the primitive streak from epiblast cells. Likewise, in stembryos cultured as described in ref. 34, a pulse of the Wnt agonist Chiron 48 h after aggregation of mES cells, that is, between 48 h…

Comment: DESeq2 remove batch effect by James W. MacDonald 63k I would reverse 1 and 2 Answer: Fishpond with unbalanced dataset by Michael Love 40k Thanks for the report, I will follow up on GH. Answer: Can DESeq2 handle low number of samples and replicates? by Michael Love 40k There…

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…

Forum:What Are The Most Common Stupid Mistakes In Bioinformatics? 78 While I of course never have stupid mistakes…ahem…I have many “friends” who: forget to check both strands generate random genomic sites without avoiding masked (NNN) gaps confuse genome freezes and even species but I’m sure there are some other very…

Statement on ethical considerations All animal work was approved and permitted by the Local Ethical Committee on Animal Experiments and conducted according to the Guidelines for Animal Experimentation recommendations (ARRIVE guidelines). In particular, mouse work related to C57BL/6NCrl mice was approved and permitted by the Institute of Molecular Genetics of…

Hi, I am a newbie to RNA-seq data analysis. I have to identify differentially expressed genes (DEGs) between human and chimpanzee in a tissue type. I have comparable RNA-seq experiment data (reads/fastq) for the two species. Each species has 2 biological replicates(each with three technical replicates) so six runs per…

BED file showing an error while performing the FPKM count in Galaxy Europe 0 When I’m running FPKM Count program in the Galaxy Europe website i’m getting an error which is a s follows: [W::hts_idx_load3] The index file is older than the data file: input.bam.bai Extract exon regions from /data/dnb08/galaxy_db/files/f/b/4/dataset_fb483fc1-0b18-4aa6-aa5c-c2b9fd8047da.dat……

Arhgef7 is required for Netrin-1–mediated commissural axon guidance. (A) The mean mRNA expression, fragments per kilobase of transcript per million mapped reads (fpkm), (± SEM) of Arhgef7 and Dcc in dissociated commissural neurons (n = 3). (B) Dissociated commissural neurons were fixed and immunostained for Arhgef7 and Dcc. Scale bar,…

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…

Count Matrix normalisation for downstream analysis and for creating heatmap of targeted genes 0 Hello Everyone! I have a count matrix generated from stringtie (from FPKM to readcount using prepDE.py3 of stringtie). i would like to create heatmap of targeted genes across samples. My questions are : 1) Before creating…

Muscle RNAseq data implicates interferon-beta in dermatomyositis (A) Selective elevation of interferon-beta (IFNB) 1 among other type 1 interferons in dermatomyositis muscle.(B) Specificity of IFNB1 elevation in dermatomyositis compared with other inflammatory myopathies and healthy muscle. RNAseq: RNA sequencing; DM: dermatomyositis; FPKM: fragments per kilobase of exon model per million reads…

ANR is relatively conserved among diarrheagenic pathogens Over the last 5 years, massive sequencing of new bacterial genomes has identified hundreds of new ANR members in multiple pathogens. ANR is widely distributed in at least 26 Gram-negative bacterial species29,31. Phylogenetic analysis of the amino acid sequence of ANR members from clinically…

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,…

How to get TPM / FPKM after batch correction with DESeq2? 1 @cfe7a460 Last seen 40 minutes ago Europe I’m trying to adjust batch effect using deseq2 limma::removeBatchEffect like below: ###### Batch Correction with limma removeBatchEffect ####### dds <- DESeqDataSetFromMatrix(countData = data, colData = coldata, design = ~ Samplebatch +…

I’m trying to adjust batch effect using deseq2 limma::removeBatchEffect and also Combat-Seq. With limma version, I can clearly see the batch effect is removed, where I see control from Batch1 is together with the other 3 controls from Batch2. ###### Batch Correction with limma removeBatchEffect ####### dds <- DESeqDataSetFromMatrix(countData =…

Ethics statement All animal experimentation was conducted according to the National Institutes of Health guidelines for the housing and care of laboratory animals. All experiments were performed in accordance with institutional regulations after review and approval by the Animal Studies Committee at Washington University School of Medicine in St Louis,…

Genomics-based consensus tumor purity estimates For TCGA samples, genomic-based consensus tumor purities were computed as a mean of predictions from ABSOLUTE17, AbsCNSeq18, ASCAT15, and PurBayes16 following the approach reported in Ghoshdastider et al. 41. AbsCNSeq and PurBayes estimates are based on mutation variant allele frequency data, and ASCAT and ABSOLUTE…

Comput Struct Biotechnol J. 2023; 21: 2276–2285. ,a,1 ,a,1 ,a ,b,c and a,b,⁎ Leiming Jiang aComputational Systems Biology Laboratory, Department of Bioinformatics, Shantou University Medical College (SUMC), 515041 Shantou, China Shijia Hao aComputational Systems Biology Laboratory, Department of Bioinformatics, Shantou University Medical College (SUMC), 515041 Shantou, China Lirui Lin aComputational…

How to Merge RNA Replicates 1 I am following the manual for a program called TimeReg that says “If there are multiple replicates, merge them to get one expression profile. For gene expression data, you may use the average expression (FPKM or TPM) of the replicates.” I have two replicates…

in an RNA-seq experiment, what threshold would you use to define a set of expressed or active genes in a cell line? 0 I am trying to define a set of expressed (active) genes in my cell line for some downstream analysis. What would be your approach for defining this…

Introduction Colorectal cancer (CRC) is a leading cause of cancer-related death1 and its mortality rate is expected to rise worldwide, due to population growth and aging, thus entailing a global public health challenge. CRC mortality is mainly due to therapy resistance and metastasis, which are driven by a small population…

Please give me a grep command to get Gene IDS and TPM values from a stringtie output gtf file 2 Hi, Could anyone please give me a grep command to get gene_id and respective TPM values from a string tie output file. My result output file looks like the following…

samtools idxstats versus samtools view command 1 Hi, I have mapped RNA-seq data to the human genome concatenated with a viral genome (26 chromosomes in total) with bowtie and need to get some numbers to calculate FPKM values manually for one viral gene, to retrieve the “total number of reads”…

Often in DE-analysis count values (FPKM or TPM) are log transformed with pseudocounts such as Log2(x+1) or Log2(x+0.1), which is done to avoid negative values. Alas, I have noticed a discrepancy I can’t get my head around. Suppose we have two expression values: 30 and 60. Using normal values, Log2FC…

Hello, I am new to bioinformatic analyses and I am trying to analyse the TCGA dataset to plot a survival curve based on the expression of a gene of interest (say TP53). I have written the following code to analyse the TCGA data, but I am unable to proceed further…

Should I use TPM or TMM to plot gene expression boxplots in RNAseq? 0 Hi all! I used $TRINITY_HOME/util/align_and_estimate_abundance.pl from trinity to do transcript quantification for my RNAseq data. Then I got the following outputs: I would like to plot the boxplots for several genes. Which one should I use….

I have a question for deg analysis tools 1 Hi. I’m going to do DEG analysis with tmp data that has already been normalized. I want to use a total of four tools; DESeq2, edgeR, Ballgown, Limma. But I already knew the raw count data can only be used in…

We aimed to assess the extent to which it was possible to effectively normalize and combine microarray and RNA-seq data with existing methods for use as a training set for machine learning applications. We assessed performance on holdout sets composed entirely of microarray data and entirely of RNA-seq data. To…

Can FPKM data sets be of any use or are they trash? 2 Hello all. I have acquired FPKM-normalized data sets (excel files) which are (supposedly) to be used for differential expression analysis. As is well known, FPKM normalization is not the best strategy in the current day and age….

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…

Ethics statement and animals All animals and experimental protocols used in this study were approved by the Beijing Institute of Animal Science, Chinese Academy of Agricultural Sciences (the scientific research department responsible for animal welfare issues) (No.: IASCAAS-AE20140615). In this study, experimental chickens (JXH) were selected on H/L, with the…

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…

Data collection and processing The RNA-sequencing data, clinical information and simple nucleotide variation of LUAD patients were retrieved from TCGA database (portal.gdc.cancer.gov/, accessed April 8, 2022). Nineteen cuproptosis-related genes (CRG) were mainly collected from previous study, including LIPT1, GLS, NFE2L2, NLRP3, LIAS, ATP7B, ATP7A, SLC31A1, FDX1, LIPT2, DLD, DLAT, PDHA1,…

Introduction Breast cancer is the most prevalent malignancy and the leading cause of cancer death in women worldwide.1 After its diagnosis, the most immediate challenge is to tailor treatment strategies and predict the prognosis; traditional clinicopathologic features, including estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2…

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…

The incidence of lung adenocarcinoma (LUAD), the most common subtype of lung cancer, continues to make lung cancer the largest cause of cancer-related deaths worldwide. Long noncoding RNAs (lncRNAs) have been shown to have a significant role in both the onset and progression of lung cancer. In this study, we…

Software official website ： Hisat2： Manual | HISAT2 StringTie：StringTie article ：Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown | Nature Protocols It is recommended to watch the nanny level tutorial ： 1. RNA-seq : Hisat2+Stringtie+DESeq2 – Hengnuo Xinzhi 2. RNA-seq use hisat2、stringtie、DESeq2 analysis – Simple books Basic usage…

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…

Introduction Lung cancer is the major leading cause of tumour-related deaths throughout the world, while lung squamous cell carcinoma (LUSC) as the second most common histological type of lung cancer.1 Each year, almost 1.8 million people are diagnosed with lung cancer worldwide and 400,000 of these die from LUSC.2,3 Due to…

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…

Difference of results with the same input [RNAseq analysis] 0 Hello! I am trying to optimize the treatment of some RNAseq files by splitting the input reads into several files. I am comparing the results I have obtained with: the reads input as one file the split input as several…

INTRODUCTION Mammalian life starts with the fusion of two terminally differentiated gametes, sperm and oocyte, resulting in a totipotent zygote. After going through preimplantation development, the zygote reaches blastocyst before implantation. The two most important events taking place during preimplantation development are zygotic genome activation (ZGA) and the first cell…

Significance The plant-specific H3K27me1 methyltransferases ATXR5 and ATXR6 play integral roles connecting epigenetic silencing with genomic stability. However, how H3K27me1 relates to these processes is poorly understood. In this study, we performed a comprehensive transcriptome analysis of tissue- and ploidy-specific expression in a hypomorphic atxr5/6 mutant and revealed that the…

Annual and perennial species occur in many plant families. Annual plants and some perennials are monocarpic (flowering once in their life cycle), characterized by a massive flowering and typically produce many seeds before the whole plant senesces. By contrast, most perennials live for many years, show delayed reproduction, and are…

What is the cutoff used for define high or low expression level of gene for survival analysis 1 Hi everyone In RNA-seq analysis, we need to separate samples into two groups for survival analysis. How can I define high level or low level for a gene according to counts or…

Hello Biostars. I obtained DEGs from RNAseq analysis for normal and infected samples. Then I decreased the number of them by some downstream analysis. Now I have 120 DEGs and I want to select between them the best combination of biomarkers that can recognize normal from infected samples (biomarker panel)….

How does Cufflinks DE calculate q-value? 5 I have run my aligned samples through the Cufflinks app in Illumina BaseSpace a couple of different ways. When I do Classic FPKM Normalization + Pairwise comparisons, I get a small list of genes. This analysis seems stringent. When I do Classic FPKM…

Introduction Gene expression is not only controlled by DNA sequences but also by epigenetic marks in eukaryotes. DNA methylation as one of the important epigenetic modifications has been demonstrated as closely related to gene expression in biological processes, such as transcriptional activity, developmental regulation, and environmental responses (Maunakea et al.,…

pre-proccessing of RNAseq data for WGCNA 0 Hi everyone, i wanted to create an expression matrix for WGCNA input. however, i has been said that use RPKM/FPKM data instead of CPM, how can i change my TCGA data to RPKM/FPKM in GDCquery and how to filter expression set of genes…

CeTF is an C/C++ implementation in R for PCIT [6] and RIF [7] algorithms, which initially were made in FORTRAN language. From these two algorithms, it was possible to integrate them in order to increase performance and Results. Input data may come from microarray, RNA-seq, or single-cell RNA-seq. The input…