Tag: RSEM

mapping – STAR error in snakemake pipeline: “EXITING because of FATAL ERROR: could not open genome file”

I’m trying to use a 2 pass STAR mapping strategy (also explained here informatics.fas.harvard.edu/rsem-example-on-odyssey.html), but I’m getting an error. I’ve read through this page [https://github.com/alexdobin/STAR/issues/181] and I have a similar issue, but the discussed solutions don’t seem to help. Perhaps this is more a snakemake issue rather than a STAR…

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In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states

Animals and sample preparation Animal experiments were performed as previously described12. C57BL/6J WT mice or ob/ob mice at ten weeks of age were purchased from Japan SLC Inc. (Shizuoka, Japan). The phenotypic data of the mice are summarized in Table S1. Animal experiments were approved by the animal ethics committee…

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Finding DEGs from HISAT2/STRINGTIE output

Finding DEGs from HISAT2/STRINGTIE output 0 Hello, I have to search for DEGs from four samples of crop. I am following reference based mapping of reads to genome using HISAT2. I have completed till the generation of merged .gtf files for the samples using STRINGTIE. Since I am new to…

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Use RSEM and Bowtie2 to align paired-end sequences

Use RSEM and Bowtie2 to align paired-end sequences 0 I want to use rsem-calculate-expression and bowtie2 aligner to align paired-end sequence based on the following conditions: 2 processors generate BAM file very fast bowtie2 sensitivity append gene/transcript name My code: rsem-refseq-extract-primary-assembly GCF_000001405.31_GRCh38.p5_genomic.fna GCF_000001405.31_GRCh38.p5_genomic.primary_assembly.fna rsem-prepare-reference –gff3 GCF_000001405.31_GRCh38.p5_genomic.gff –bowtie2 –bowtie2-path /bowtie2-2.4.5-py39hd2f7db1_2 –trusted-sources…

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Bioinformatics analysis identifies widely expressed genes

1Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China; 2Department of Pediatrics, The Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China Correspondence: Jun Qian, Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui,…

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how to build index for cdna?

Hello, I can build index for Mus_musculus.GRCm38.dna_sm.toplevel.fa, but when build for Mus_musculus.GRCm38.cdna.all.fa, there is a bug: “rsem-extract-reference-transcripts Mus_musculus.GRCm38.cdna.all.fa 0 Mus_musculus.GRCm38.cdna.all.fa.gtf None 0 Mus_musculus.GRCm38.cdna.all” failed! Plase check if you provide correct parameters/options for the pipeline! Traceback (most recent call last): File “../indrops.py”, line 1770, in project.build_transcriptome(args.genome_fasta_gz, args.ensembl_gtf_gz, mode=args.mode) File “../indrops.py”, line…

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RNAseq data DEG analysis – DESeq2 normalized data

RNAseq data DEG analysis – DESeq2 normalized data 1 1) You can’t use because those data are already normalized and log-transformed. 3) RSEM expected_count is best to start off with for differential expression. Login before adding your answer. Traffic: 2089 users visited in the last hour Read more here: Source…

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3 -tag XM” failed! when running rsem-calculate-expression

Dear sir, When I ran “rsem-calculate-expression –paired-end –alignments -p 8input.bam” gencodev22 ./out. I got error message rsem-parse-alignments ../bowtie2/hg38 ./rsem-out.temp/rsem-out ./rsem-out.stat/rsem-out /NGS_Storage/Debbie/RNA-seq/variant_calling_20210602/RNA-leukemia002A-906.para.bam 3 -tag XM Read A00355:209:H3KTLDSX2:2:2606:24677:17425: The adjacent two lines do not represent the two mates of a paired-end read! (RSEM assumes the two mates of a paired-end read should…

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rsem-calculate-expression error /lib/libc.so.6: version `GLIBC_2.14′ not found

Hi, When I run rsem-calculate-expression. I got an error like this: $ home/trinityrnaseq/trinity-plugins/rsem/rsem-parse-alignments /home/trinityrnaseq/trinity-plugins/rsem/rsem-parse-alignments: /lib/libc.so.6: version GLIBC_2.15′ not found (required by /home/trinityrnaseq/trinity-plugins/rsem/rsem-parse-alignments) /home/trinityrnaseq/trinity-plugins/rsem/rsem-parse-alignments: /lib/libc.so.6: version GLIBC_2.14′ not found (required by /home/trinityrnaseq/trinity-plugins/rsem/rsem-parse-alignments) Any help would be greatly appreciated~~ Read more here: Source link

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How to reduce the impact of one varaible in Deseq2 or edgeR for multivariate value analysis?

Hello, everyone, I’m recently meeting this problem with my analysis, which i’ve done a lots of research and asked people around but their answers are quite confusing, so if I can get more opinions, that’d be terrific and thanks at advance. So I’m doing an analysis of DEGs using Deseq2…

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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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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 …

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

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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