Tag: TPM

Dear All, my question is related to this post: Error in while (change > conv) { : missing value where TRUE/FALSE needed I have a heterogeneous RNAseq dataset in TPMs from 66 samples and two sequencing batches (64 from one batch, 2 from the second batch). This dataset contains many…

The panel (A) refers to the four known cases (Venturia canescens, Fopius arisanus, Cotesia congregata, and Microplitis demolitor) involving Nudivirus donors while the panel (B) refers to the known case involving LbFV donors in three Leptopilina species. Complete parasitoid wasp genomes information was available for Microplitis demolitor, Venturia canescens, Fopius…

How to calculate TPM from featureCounts output 0 I would like to find the TPM counts for the GSE102073 study. When i downloaded the raw data from GEO, the raw data are featureCounts output. First part of the file: # Program:featureCounts v1.4.3-p1; Command:”/data/NYGC/Software/Subread/subread-1.4.3-p1-Linux-x86_64/bin/featureCounts” “-s” “2” “-a” “/data/NYGC/Resources/ENCODE/Gencode/gencode.v18.annotation.gtf” “-o” “/data/analysis/LevineD/Project_LEV_01204_RNA_2014-01-30/Sample_JB4853/featureCounts/Sample_JB4853_counts.txt” “/data/analysis/LevineD/Project_LEV_01204_RNA_2014-01-30/Sample_JB4853/STAR_alignment/Sample_JB4853_Aligned.out.WithReadGroup.sorted.bam”…

RNAseq (HiSeq, Gene level, Tumor) Download RNAseq data RSEM upper-quartile normalized (Illumina HiSeq platform, Gene-level) gene Expression (RSEM-UQ, Log2(Val+1)) 140 28057 cct RNAseq (HiSeq, Gene level, Normal) Download RNAseq data RSEM upper-quartile normalized (Illumina HiSeq platform, Gene-level) gene Expression (RSEM-UQ, Log2(Val+1)) 21 28057 cct RNAseq (HiSeq, Gene level, Duct) Download…

WGCNA: many over and under-expressed features in modules of a signed network 1 In a WGCNA analysis of transcriptome and proteome of a white blood cell in development (in 6 stages), I find in most modules (especially the large ones) over, as well as underexpressed features, but I am using…

What type of normalization did they use in this article? 1 I’ve read this amazing article, yet I’m struggling to understand how did they normalize the bulk RNA-seq data. I’ve downloaded the data from the supplementary information, and the values of all the genes are around 30, so this can’t…

Graphing Average Expression of Group of Genes 0 I’m trying to plot the expression of a group of genes over time. My starting dataframe is in TPM like below. V1 MEF DAY3 DAY6 DAY9 DAY12 IPSC Arhgef12 48.9061752 76.001558 64.294236 61.0208545 66.4678191 25.11639309 Arnt2 8.6570850 11.341789 22.613930 35.2099605 36.0336247 1.30568627…

What is the best way to clean bulk RNA-seq data? 1 As far as I know, there isn’t a universally agreed-upon threshold or an approach to clean the data. I want to remove the genes that don’t contribute, or in other words, the noise genes, BEFORE I normalize the data,…

Two ASX health stocks had double-digit share price jumps on Monday morning, after positive US Food and Drug Administration moves. Meanwhile two other companies have also delivered good news. For the latest health news, sign up here for free Stockhead daily newsletters Tissue Repair to progress to Phase 3 Wound…

Does the RNAseq data normal if the TPM value 3rd Qutile expression is near 10, but the Max expression are near 20,000 1 Dear all, May I have your guidance that the gene expression TPM as below is normal? The most highly expressed seems all correlated with Ribonucle, if filter…

Mapping of bulk RNA-seq data and differential gene expression (DGE) Using the splice-aware aligner STAR, we mapped the RNA-seq reads to the H. bakeri genome assembly obtained from WormBase ParaSite (PRJEB15396). Among all the datasets, 93.26–95.62% of the reads uniquely mapped to the reference genome (Table 1), reflecting the high…

Hello, I want to compare (with a PCA) gene expression against copy number variation at gene level in a TCGA project.When I retrieve the gene expression every value is mapped by sample and gene. But for the copy number variation, I get only chromosomal locations.To do the PCA, I want…

Is the gene-specific PCR efficiency a serious concern for intrasample comparisons in RNA-Seq? 1 Or “Everything You Always Wanted to Know About RNA-Seq (But Were Afraid to Ask) Part 2” In RNA-Seq, it is common practice to compare the abundance of transcripts within the same sample after some form of…

Normalizing RNA read counts for each gene? 2 While reading a paper, I encountered the line “Heatmap of normalized read counts for chlorophyll-protein complexes (LHCs) normalized by row to reflect relative expression of each gene (see scale bar)” and was wondering if someone would be able to clarify how the…

The abundance and composition of prokaryotes carrying antiviral system in DWDS microbiome Prokaryotes have evolved various defense systems to prevent virus infection and prophage activation [8]. DefenseFinder revealed various prokaryotic antiviral systems harbored by the drinking water microbiome [9], and PCoA analysis showed that prokaryotic antiviral systems clustered separately in…

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…

Genecount-difference between HT-seq count, RSEM, and Kallisto 0 Hi I ran three genecount software tools (ht-seq, RSEM, Kallisto) to calculate genecount of RNA-seq data. For Ht-seq, i used STAR aligned Transcriptomesortedcordinate.bam file and defautl MAPQ score with intersection_nonempty mode. For RSEM, i used STAR aligner (used .gtf for building reference)…

Tumor-infiltrating immune cells 1 Hi, I have a list of genes and samples which got from TCGA in STAR count format and normalize them with edgeR and limma packages, now I want to assess Tumor-infiltrating immune cells, I try TIMER v2, but the input in this site should be TPM-normalized…

Hello everyone, Initially I express that I am not very expert in bioinformatics analysis. I have the TMP from RNAseq data. These data come from Arabidopsis seeds infected with a fungal inoculum. I select the data by calculating the zscore. Thanks to the tutorials and the forums I have managed…

RMA Normalization & Units 0 I’m working on doing some analysis of drug response in cell lines, specifically the genomics of drug sensitivity in cancer (GDSC). In downloading from the source (www.cancerrxgene.org/gdsc1000/GDSC1000_WebResources/Home.html) the expression data is described as “RMA normalised basal expression profiles for all the cell-lines.” Most of my…

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,…

Is there anyway to cancel CPM normalization? 1 I am performing a meta-analysis and I am looking for processed RNA-seq data. I would prefer counts data, but if that is not available, then TPM normalized data would be acceptable. I found a dataset that only has logCPM normalized RNA-seq data…

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 +…

Hey guys. Good afternoon. I would like to separate the TCGA-STAD data into two groups, one with high expression for gene x, and one with low expression for gene x. I would like to separate these groups according to quartiles, taking the upper and lower quartiles. Then, I would perform…

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 =…

The TRACERx 421 cohort The TRACERx study (clinicaltrials.gov/ct2/show/NCT01888601) is a prospective observational cohort study that aims to transform our understanding of NSCLC, the design of which has been approved by an independent research ethics committee (13/LO/1546). Informed consent for entry into the TRACERx study was mandatory and obtained from every…

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…

Multiple H2BNTac sites occupy the same genomic regions H2BNTac sites are similarly regulated by CBP/p30018 (Supplementary Fig. 1a), yet the reported genome occupancy patterns of H2BNTac sites are dissimilar from each other22,23 (Supplementary Note 1). To resolve this conundrum, we systematically compared H3K27ac and H2BNTac genomic occupancy and regulation by…

Non-zero expression counts from deleted genes 0 Hi all, I’ve been looking at the RNA-seq data (STAR counts) for homozygously deleted genes (ASCAT copy number = 0) in TCGA and don’t understand what I’m seeing. I expected these genes to have zero or negligible TPMs, but actually the vast majority…

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…

Hi wes, Yes, basically the TPM information and gene names are enough to produce similar boxplots. TPM is already a normalized method so you don’t need to log transform the expression. For the plots, you just need to load the expression matrix and select the hub genes and then plot….

Cell line expression of tumor-specific TE-chimeric transcripts. a, Box plots with overlaid dot plots of the number of candidates expressed in each cancer cell line profiled across various tumor types. The ‘N=’ lists the number of cell lines in each boxplot. Box plot format: center line, median; box limits, upper…

I have a signature composed of several genes, but not all the genes work in the same direction. In order to predict the outcome with my signature, some of them should be highly expressed while others should be lowly expressed. Generating a gsva as a summary of the expression seems…

Do we need replicates for PSI calculation in SUPPA2? 0 Hi, I don’t have replicates for my RNA-seq experiment. However, I have 6 samples and six controls from different plants. I am trying to perform Alternative splicing analysis and have generated All splicing events using SUPPA2 event generator. However, I…

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…

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…

salmon output interpretation 0 Hi salmon users, Can someone help me interpret salmon output? I ran salmon with one short read sample and see most of its TPM level is 0. I see 150653 among, 252045 is 0. Does this mean, for this specific sample, it’s relative transcript abundance is…

GWAS-level and post-GWAS analyses GWAS of PD have nominated 90 independent risk signals in individuals of European ancestry, explaining ~16–36% of the heritable risk7, as well as two additional risk signals in Asian populations8. Typically, published GWAS are accompanied by various follow-up analyses, but performing these analyses is not always…

ggmodelPlot {glmmSeq} R Documentation Mixed model effects plot using ggplot2 Description Plot to show differences between groups and over time using ggplot2. Usage ggmodelPlot( object, geneName = NULL, x1var = NULL, x2var = NULL, x2shift = NULL, xlab = NULL, ylab = geneName, plab = NULL, title = geneName, logTransform…

long read + salmon? (transcript abundance) 2 Hi all, Are there any tools that can quantify transcript abundance (e.g. TPM) from long read? As far as I know, salmon only works with short read data. salmon read long • 63 views • link updated 1 hour ago by Rob 5.8k…

Batch effect in integrated RNA-seq analysis 1 Hi, I’m beginner in bioinformatic as PhD candidate in Japan. I am trying to do an integrating bulk RNA-seq analysis using some public transcriptomic data from multiple facilities, but I’m struggling with batch effect correction. When I try to draw heatmap using TPM…

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…

Salmon TPM calculation constant 1 Hi all, salmon seems to calculate the TPM using the equation below, and looks like the constant is 26.1 for every calculated TPM. Does anybody know what this constant means and how it’s derived? TPM = constant * NumReads / EffectiveLength, salmon TPM • 44…

Genome reduction is associated with a termite comb-associated lifestyle For our studies, we collected fungus comb samples originating from mounds of Macrotermes natalensis, Odontotermes spp., and Microtermes spp. termites and were able to obtain seven viable Pseudoxylaria cultures (X802 [Microtermes sp.], Mn132, Mn153, X187, X3-2 [Macrotermes natalensis], and X167, X170LB [Odontotermes…

Intron retention gene expression using salmon 0 I have a list of intron retention found in my short read data. I want to see if those intron retentions are lowly expressed. Can somebody comment on my experiment step if this is correct? Run my data (bam file) using salmon Sum…

NEW YORK – Bioinformatics company Allelica said on Wednesday that it is collaborating with Taiwanese precision medicine firm SP BioMed on a polygenic risk score (PRS) study of breast cancer. The goal of the study is to determine the best genotyping technology for genome-wide data generation for future applications such…

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…

Third quartile normalized logFC data to find differentially express gene using limma 0 I have normalized count matrix which is normalized using conditional quantile normalization and having negative value, I understand that these are normalized logFC values. When I am directly using into limma with following command. It is showing…

The Trem2 R47H NSS mutation promotes loss of oligodendrocyte gene expression in response to cuprizone treatment. Results of previous studies of mice with the Trem2R47H missense mutation introduced via CRISPR suggested that it acts as a near-complete loss of function, recapitulating phenotypes seen in Trem2 knock-out (KO) mice [34, 36]….

Renormalize after row/column deletion from TPM data in RNA-seq 1 I am working with single-cell data and received the TPM-normalized RNA-seq dataset from my labmate. Once I remove genes or cells during preprocessing, I notice that the data is no longer normalized (colSums from R is not returning 1e06). Is…

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…

I have counts data (processed already) and I want to get the lengths of the genes from Biomart, in order to normalize the data to TPM. I’ve done this already many times in the past, and now I have new data, with 50K genes. This is the code, and it…

Hi all, I ran into an edge case situation of kallisto not processing GENCODE transcript identifiers correctly, and this currently propagates into tximport. Ideally this should be fixed upstream in kallisto, but we should harden tximport against this situation. Here’s an example kallisto run aligned against GENCODE that is problematic:…

Tutorial:Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq 1 ## Load the required library library(‘TCGAbiolinks’) project_name <- “TCGA-ACC” ## Defines the query to the GDC query <- GDCquery(project = project_name, data.category = “Transcriptome Profiling”, data.type = “Gene Expression Quantification”, experimental.strategy = “RNA-Seq”, workflow.type = “STAR – Counts”)…

How do I go from TPM to PCA (rna-seq)? 1 Hello all, I am new to rna-seq analysis. I have abundance TPM information (kallisto output, from 400+ samples). I just want to perform clustering analysis? How do I go from TPM data to PCA and other rna-seq? Is there any…

Which input file is used for DGEList in EgdeR? 1 @mohammedtoufiq91-17679 Last seen 1 day ago Qatar Hi, I used an nf-core/rnaseq pipeline using star_salmon default aligner, on strand specific dataset. I have a question about gene counts data obtained as a result of salmon quantification. I am interested in…

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…

mosdepth coverage & transcripts per million 0 Hi all, I recently ran MosDepth on my functionally annotated MAGs to calculate the coverage for each gene found in each MAG bin. I was wondering if anyone could help me figure out how to convert the coverage calculated by MosDepth (which calculates…

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…

Different summary() and results() values in DeSeq2 2 @e7ba24a7 Last seen 2 hours ago Germany I have run DeSeq2 in 2 different devices using the same count data and metadata tables, however when running the summary and results I get different values. I made sure the files are read correctly,…

How to normalize long-read RNA-seq data for comparison with short-reads 1 I am working on a project comparing RNAseq quantification results between Illumina short-reads and Nanopore long-reads and I have a couple questions about comparing the quantification results from these two technologies. More specifically I need some help with figuring…

The landscape of somatic mutation in normal human small intestinal crypts The base of each small intestinal crypt is occupied by stem cells, and the descendants of a single recent ancestor stem cell comprise most cells in each crypt19,20. Therefore, isolation of single crypts provides relatively homogeneous clones of cells…

Normalizing TCR data 1 Hi, What’s the best method to normalize TCR repertoire data (for comparison between samples) which already has raw counts and count frequency. Already tried Counts per Million (CPM) but there’s a possibility that it might exaggerate the count number of a clone so the real picture…

Which RUVr batch corrected output is better to calculate TPM? 0 I have downloaded several samples from 5 studies (5 batches). Example of my count table: S_rep1_batch1 S_rep2_batch1 S_rep1_batch2 S_rep2_batch2 S_rep3_batch2 . . . Gene1 34 54 65 76 67 Gene2 87 77 90 35 19 Gene3 47 67 70…

RNA-seq library size – significant sample discrepency 2 Hello, I’ve been given some data to perform differential expression on, and it the process of QCing the resultant count data, I’m seeing that the library sizes have pretty big discrepancies between the 2 samples shown below. I know a good run…

Hello all, I have a code that is supposed to read a file ‘filecontig,’ take all the sequence IDs within that file, match those IDs to IDs in files ‘filetaxa’ and ‘fileTPM’ and output the taxonomical classifications as well as the transcripts per million that match each respective ID. I…

How to download eQTLS data for the Long Read RNASeq data (Glinos et. al., bioRxiv, 2021). 0 0 Entering edit mode 21 hours ago tulika • 0 Hi all, I have downloaded the TPM data for brain tissue from GTeX portal (www.gtexportal.org/home/datasets). I want the corresponding eQTLS data. Do anyone…

Manually calculating log2 fold change values from DESeq2 normalized counts 1 I need to calculate log2 fold change values for lot of different experimental conditions when compared to their corresponding controls. Just to mention, I am not going to use these for differential expression analysis but for some other downstream…

Normalizing Salmon output count data matrix using DESeq2 1 @7cabb0d9 Last seen 12 hours ago United States I import counts and abundance matrix from Salmon output using tximport. I want to normalize the Salmon output count matrix using DESeq2 package. What code should I use to achieve this task? Can…

Import quant.sf files 0 Hi, I have a problem in importing quant.sf files. I’ve already read a lot of posts, but I can’t solve the issue. I have ~600 quant.sf files obtained from Dragen RNA analysis and they are all in the same folder. I would like to import them…

The gene expression of Mamu-E is regulated by extensive alternative splicing that is conserved among HLA-E isoforms To accurately define Mamu-E transcript structures, we aimed to use high-quality, full-length transcript sequences obtained by long-read transcriptome sequencing41. Since the sequences of MHC genes are very similar, it was critical that we…

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…

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…

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…

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 &starf;…

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…

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…

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…

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)…

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…

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…

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…

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…

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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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…

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…

—–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…

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…

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…

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…

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)….

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…

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…

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)…

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…

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…

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…

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…