Tag: RSEM

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…

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Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet

1. Singh, A. et al. Phytochemical profile of sugarcane and its potential health aspects. Pharmacogn. Rev. 9, 45–54 (2015). CAS  PubMed  PubMed Central  Google Scholar  2. Eggleston, G. Positive aspects of cane sugar and sugar cane derived products in food and nutrition. J. Agric. Food Chem. 66, 4007–4012 (2018). CAS …

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rsem-calculate-expression with STAR takes forever but without error

rsem-calculate-expression with STAR takes forever but without error 1 Hi all, I am running rsem-calculate-expression after succesfully generating the reference files with rsem-prepare-reference. However, the command never proceeds past: “started mapping” like in the example below Sep 16 08:44:43 ….. started STAR run Sep 16 08:44:43 ….. loading genome Sep…

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STAR+RSEM pippline without gtf

STAR+RSEM pippline without gtf 0 Dear all, I have question I mapped reads on cds sequence through STAR I don’t have gtf file and want to calculate read count using RSEM but I am stuck by error “RSEM error: RSEM currently does not support gapped alignments” as I don’t have…

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Download TCGA and GTEX data from Xena toilHub for (full genome but for 1 cancer/tissue type)

Download TCGA and GTEX data from Xena toilHub for (full genome but for 1 cancer/tissue type) 0 Dear All, I would like to download TCGA and GTEX gene expression data for ovarian cancer and ovary respectively from the Xena toilHub platform (all genes; RSEM expected counts). However, I only found…

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Survival analysis for a list of genes using TCGA data

Survival analysis for a list of genes using TCGA data 1 Hi all, I have a list of genes (around 300 genes) and I want survival analysis to find only significant genes. I am using TCGA RSEM normalized data in survival package using following command, but I’m not sure how…

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pughlab/inspire-genomics: Pan-cancer analysis of genomic and immune landscape profiles of metastatic solid tumors treated with pembrolizumab

Contents Serial circulating tumor DNA (ctDNA) monitoring is emerging as a non-invasive strategy to predict and monitor immune checkpoint blockade (ICB) therapeutic efficacy across cancer types. Yet, limited data exist to show the relationship between ctDNA dynamics and tumor genome and immune microenvironment in patients receiving ICB. Here, we present…

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regarding coexpression analysis (by pearson method) of genes shortlisted from expression profile of a dataset obtained from GDAC Firehouse database

regarding coexpression analysis (by pearson method) of genes shortlisted from expression profile of a dataset obtained from GDAC Firehouse database 0 Hello guys, Should i consider genes having “zero” normalized count given in expression data of a dataset while doing coexpression analysis with respect to a particular gene (whose expression…

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Bioconductor Forum

James W. MacDonald 57k 1 week, 5 days ago United States Answer: Biomart’s getBM returns no genes for an existing GO-term in grch38, and less the Michael Love 33k 1 week, 6 days ago United States Answer: Normalizing 5′ Nascent RNA-seq data to identify differentially expressed transcr Kevin Blighe 3.3k 2 weeks, 2 days ago Republic…

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rsem-prepare-reference –allele-to-gene-map (file information required)

rsem-prepare-reference –allele-to-gene-map <file> (file information required) 0 –allele-to-gene-map <file>Use information from <file> to provide gene_id and transcript_id information for each allele-specific transcript. Each line of <file> should be of the form: gene_id transcript_id allele_id with the fields separated by a tab character. This option is designed for quantifying allele-specific expression….

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