Tag: TPM

Expression level of mutant genes in RNAseq data

Expression level of mutant genes in RNAseq data 1 Hello, I have WES data from matched tumor and normal samples and mutants called from these data (in MAF files). From my understanding, if I sequence the tumor sample RNA, and run a routine RNAseq data analysis pipeline, the counts I…

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Genomic signatures associated with maintenance of genome stability and venom turnover in two parasitoid wasps

Genomic features of two Anastatus wasps, A. japonicus and A. fulloi We employed PacBio high-fidelity (HiFi) long-read sequencing and Illumina short-read sequencing technologies to generate high-quality contigs for two Anastatus wasps, A. japonicus and A. fulloi (Supplementary Tables 1 and 2). These contigs were further scaffolded using Hi-C libraries to…

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Comprehensive Analysis of NPSR1-AS1 as a Novel Diagnostic and Prognostic Biomarker Involved in Immune Infiltrates in Lung Adenocarcinoma

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…

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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 ★…

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Subtype and cell type specific expression of lncRNAs provide insight into breast cancer

lncRNA expression according to breast cancer clinicopathological subtypes To identify lncRNAs expressed by specific breast cancer subtypes or associated with clinicopathological features, we analyzed RNA-sequencing data from two large independent breast cancer cohorts: SCAN-B (n = 3455)17 and TCGA-BRCA (n = 1095). We focused on lncRNAs annotated in the Ensembl18 v93 non-coding reference transcriptome…

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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…

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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…

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Nitrogen cycling and microbial cooperation in the terrestrial subsurface

Distribution of nitrogen-cycling pathways in groundwater Differences in nitrogen-cycling processes based on oxygen and nitrate concentrations Sixteen metagenomes (Table S4) were obtained from duplicate wells at four sites (A–D) from two unconfined alluvial aquifers (Canterbury, Fig. S1). These sites encompassed varied nitrate (0.45–12.6 g/m3), DO (0.37–7.5 mg/L), and dissolved organic carbon (DOC) (0–26 g/m3)…

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Negative values after batch correction using removeBatchEffect from Limma

I am trying to correct my RNA seq data for 3 categorical variables as well as preserve the biological information of the dataset. In order to do that, I have used the removeBatchEffect function from limma. I used a log2(TPM counts + 1) matrix as my input but… as you…

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Hisat2 – stringtie – deseq2 pipeline for bulk RNA seq

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…

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Transcriptomic and proteomic profiling of peptidase expression in Fasciola hepatica eggs developing at host’s body temperature

From the bovine liver, we isolated 97 live F. hepatica adults. After overnight cultivation, we recovered approx. 228,000 laid eggs, which we divided in three groups. The first group (T0) was immediately frozen at − 80 °C, while the other two groups (T5 and T10) were incubated for 5 and 10 days at…

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rna seq – How will Seurat handle pre-normalized and pre-scaled data?

I don’t do transcriptome analysis, it ain’t my thing, however I do understand statistical analysis as well as the underlying issue regarding the public availability of molecular data … I agree with the OP its not ideal. However, yes the OP can continue with ‘clustering’, personally I definitely prefer it…

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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,…

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google careers ADM

google data scientist certificate careers at google canada google applied jobs google hiring 2022 google ads specialist hiring hiring in google google company recruitment 2021 google frontend developer google reviewer job google philanthropy jobs machine learning developer google google bioinformatics jobs google android developer jobs google attorney jobs google pm…

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Katia Feve – Academia.edu

Katia Feve – Academia.edu Academia.edu no longer supports Internet Explorer. To browse Academia.edu and the wider internet faster and more securely, please take a few seconds to upgrade your browser. Academia.edu uses cookies to personalize content, tailor ads and improve the user experience. By using our site, you agree to our…

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CIBERSORTxFractions ERROR: Could not read /src/outdir//temp.Fractions.simfracs.tsv

Hello, can anyone offer any insight into the following problem? I am trying to run the following CIBERSORTx function locally: docker run -v /media/mark/seagate2/data/CIBERSORTx_GC:/src/data -v /media/mark/seagate2/data/CIBERSORTx_GC:/src/outdir cibersortx/fractions –username <my_user_name> –token <my_token> –single_cell TRUE –refsample reference.txt –mixture rsem_mixture_TPM.tsv –fraction 0 –rmbatchSmode TRUE I get the following output to the terminal: >Running…

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Accepted drop-seq 2.5.1+dfsg-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Sun, 16 Jan 2022 16:45:58 +0100 Source: drop-seq Architecture: source Version: 2.5.1+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Andreas Tille <ti…@debian.org> Changes: drop-seq (2.5.1+dfsg-1) unstable; urgency=medium . * New upstream version * Add missing build dependency…

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r – ggplot: Try to plot boxplots with geom_rect on its background, but keep having error with object “variable” not found

I was almost desperate with this error after working on this for 4 hrs, googled and looked from past posts already. Here is my data structure: str(tcga_exp) ‘data.frame’: 11775 obs. of 5 variables: $ cohort: chr “BRCA-Basal.Tumor” “BRCA-LumA.Tumor” “BRCA-LumB.Tumor” “BRCA-LumA.Tumor” … $ exp : num 6.35 5.54 6.56 5.05 5.98…

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Help needed for Ensembl Gene ID conversion for RNA-seq data

Hello All, I am new to the RNA-seq world and especially new to the bioinformatics side. We recently completed a RNA-seq experiment (total RNAs) on human samples and we used illumina’s Dragen RNA pipeline which generated salmon gene count (.sf) output files. In the files, the gene ID is in…

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TPM value from DESE2 and significant filterig isssue

TPM value from DESE2 and significant filterig isssue 0 The code 10101 res_ddsDE_new has 36,000 rows. When I am using subset(res_ddsDE_new, padj < 0.05 & abs(log2FoldChange) > 1) res_ddsDE_new baseMean log2FoldChange <numeric> <numeric> DDX11L1 1.779144 -1.4955939 WASH7P 152.518293 -0.0505911 MIR6859-1 20.653876 0.5689275 MIR1302-2HG 0.255387 -1.9691031 FAM138A 0.353478 0.1574042 Then I…

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Using machine learning methods to find a biomarker panel to diagnose a disease.

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)….

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Statistics on RNAseq data

Statistics on RNAseq data 2 Hi I would like to know whether you can do statistical tests (e.g. ANOVAS etc.) on the TPM/RPKM counts of RNAseq data? Thanks on Statistics data RNAseq • 58 views This is not recommended due to a few underlying problems with RNA-seq data that include…

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Different Gene Lengths and Expected Gene Lengths from Sample to Sample

Different Gene Lengths and Expected Gene Lengths from Sample to Sample 0 Hi all, I have come across something I have never seen before. I am working with some data from an outside source which appears to be processed RNA-seq files. Like other processed RNA-seq files I have ran into…

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Transcriptional noise detection and Salmon TPMs

Transcriptional noise detection and Salmon TPMs 1 Hello, I’m analysing RNA-seq data from two datasets (from healthy samples) and created a unique GTF file to identify new isoforms by using StringTie. Then I used Salmon to estimate their TPMs, but I have some questions hoping anyone can help me: 1)…

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CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysis | BMC Genomics

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…

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DESeq2 with a small number of genes

DESeq2 with a small number of genes 1 Dear all, I am writing a program in order to study the coverage of only one sequence. To sum up the pipeline: Detect ORFs in the input sequence Align all reads on the sequence (bowtie), reads come from RNA-seq Count the number…

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Whether the probe intensity of microarray can be used to calculate TPM like the count data of RNAseq?

Whether the probe intensity of microarray can be used to calculate TPM like the count data of RNAseq? 1 Hello everyone! I’m using a software that requires TPM. But I can’t find enough RNAseq data to do analysis at the moment. I have downloaded some microarray data from a database…

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Calculate TPM values from DESeq2 normalised counts

Calculate TPM values from DESeq2 normalised counts 0 Hi all! Still somewhat new to handling transcriptomic data, and have a newbie question. I’m just trying to convert some RNA-Seq count data to TPM for the purpose of presenting qualitative comparisons about relative expression of various genes in a single cell…

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When importing my quant.sf files into R using tximport, should I set ‘ignoreTxVersion’ to True or False?

Hello, I’m working through my first batch of RNA-Seq analysis and unfortunately I don’t have an experienced bioinformatician to work with. My question is regarding tximport of my quant.sf files into R. I have been working with the EquCab3.0 reference transcriptome from NCBI to generate these quant.sf files, but I…

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How does miRdeep2 normalise sequences

How does miRdeep2 normalise sequences 1 Hi, I have mirdeep2 output that looks like this. #miRNA read_count precursor total seq seq(norm) mmu-let-7a-5p 43271 mmu-let-7a-1 43271 43271 7658.26 mmu-let-7a-1-3p 784 mmu-let-7a-1 784 784 138.76 mmu-let-7a-5p 43224 mmu-let-7a-2 43224 43224 7649.94 I think using the seq(norm) would be appropriate, but I cannot…

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Gene co-expression in single-cell RNA-seq

Gene co-expression in single-cell RNA-seq 0 I am using single-cell RNA-seq data from the Allen Institute, and I want to look at gene co-expression in different cell populations. They provide raw UMI counts, so I’m wondering what normalization method to use (e.g., CPM, TPM, VST) to look at these correlations….

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Normalisation for single nuclei RNA-seq

Normalisation for single nuclei RNA-seq 0 For single cell RNA-seq the typical workflow includes a normalisation step to account for variable sequencing depth. In Scanpy/Seurat, CPM (Counts per million) is a simple and common choice. We don’t normally normalize for gene length (like we would with full length transcript bulk…

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TPM to logFC and pvalues

Hi, I assume you have to find differential expression between two cell lines (Cx and Dx groups). Since you need logFC and Pvalue, this R code can work. And you can use obtained matrix (mysample) to calculate FDR of your interest. mysample <- read.table(“./mymatrix.csv”, sep=”,”, header=TRUE) for(i in 2:nrow(mysample)) {…

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