Tag: RSEM

Obtain a –gene-trans-map file after rnaSPAdes 0 Hello, I would like to perform a differential gene analysis on a dataset of 120 paird-end files. I obtained a good de novo quality metatranscriptome using rnaSPAdes (83% of the reads aligned exactly 1 time with bowtie2). I would now like to quantify…

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…

Alignment of case vs. control from different origin 0 Hi Biostars! I am coming to you with a relatively simple question, but one that i have surprisingly not found and answer to. I am working with a case-cohort of samples that were prepared for RNA-seq as paired reads with a…

RNAseq Data and Pipeline 1 Hello, I am currently trying to do differential gene expression with TCGA data imported with R (GDCquery). I want to utilize DESeq2 as it is widely used and want publication quality results. I am struggling to understand where “raw” counts are found for star –…

Counting intronic reads in bulk RNA-seq 0 My experience with single-cell RNA-seq shows that the inclusion of intronic reads improves the sensitivity for several genes of interest, which otherwise have zero expression when only exonic reads are considered. While single-cell sequencing quantifiers now often have options to count intronic reads,…

How does salmon uses polyester? 1 Hi Salmon users or developers! In salmon paper, to evaluate the ground truth, it uses RSEM to a certain data and uses polyester to the output of RSEM. Why use polyester on the output of RSEM? In salmon github repo, can somebody direct me…

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)…

Issue running RSEM 0 I am trying to run RSEM on my output from STAR. I have vreated the RSEM ref and have it in my working diretory, however when I run RSEM: rsem-calculate-expression –paired-end –bam -p 16 “$f” RSEMref/ rsem_out/”$base” I get this error: rsem-parse-alignments RSEMref/ rsem_out/MR13_S13.temp/MR13_S13 rsem_out/MR13_S13.stat/MR13_S13 MR13_S13_mappedAligned.toTranscriptome.out.bam…

Read counting in RSEM and Salmon (alignment mode) 1 Hi all, I was wondering if someone can clarify an issue for me. When counting reads for RNA-seq, you can use EM-based algorithms to correctly assign multimapping reads. Thus, if you have 5 single-end reads that map to 1 transcript, and…

Cell culture and reagents Non-cancerous mammary epithelium cell (MCF10A), breast cancer cells including luminal (MCF7, MDA-MB-361, T47D, and BT474), HER2amp (SKBR3), and triple-negative (MDA-MB-231, CAL51, BT20, and MDA-MB-468) subtypes, as well as human embryonic kidney 293T (HEK-293T) cells, were purchased from the American Type Culture Collection (Manassas, VA, USA). MDA-MB-231,…

Focal ablation technologies are routinely used in the clinical management of inoperable solid tumors but often result in incomplete ablations leading to high recurrence rates. Adjuvant therapies capable of safely eliminating residual tumor cells are therefore of great clinical interest. Interleukin 12 (IL-12) is a potent antitumor cytokine that can…

RSEM expression values 0 In RSEM.isoform.TMM.EXPR.matrix, some values for a set of 3 samples are like this: 0.596 0.782 0 2.173 0 0 4465.372 3953.622 5033.097 Why there is so much difference between samples and among different transcripts? RSem expression Quantification Trinity • 26 views Login before adding your answer….

Nextflow rnaseq finishing early 0 Hi I’m running the RNA-seq pipeline from nextflow and I have been running it without problems until this dataset it just stops prematurely saying it has finished when it doesn’t even aligns the reads with salmon. Any ideas what may be going on? I have…

Can I run DESeq2 with SMART-Seq data 1 @assa-yeroslaviz-1597 Last seen 2 days ago Germany my data set comes from single-cell SMART-Seq data, where I have in total 48 samples, 24 samples for the control and 24 for my KO. Each sample represent one cell. I have used STAR to…

Add HI:i:<n> tag to a BAM file 0 Hi all, I’ve been using STAR in conjunction with RSEM to get the most accurate quantification of RNA-seq for a while now. However, in one of the recent projects, I needed to map reads to a repetitive reference, generating an alignment with…

Converting an output de-novo transcriptome assembled with Trinity to a .gff3 file 2 Hello! I’ve de-novo assembled a transcriptome from Trinity, resulting into Trinity.fasta, whose headers look like this: >TRINITY_DN29256_c0_g1_i1 len=323 path=[0:0-322] Followed, in the next line, by the sequence. To run an external downstream analysis with a R script,…

Empty genes.bam files in RSEM-STAR workflow 0 This question concerns an RNAseq data aligment and transcript quantification step that generates empty bam files but still generates counts file. I would love to know 1. If the count data is reliable if bam files are empty ? and 2. How can…

The solution to this is within the `Samples.mRNASeq` that gives data which can be saved in JSON format: [0] { cohort “ACC”, expression_log2 3.635731, gene “CD274”, geneID 29126, protocol “RSEM”, sample_type “TP”, tcga_participant_barcode “TCGA-PK-A5HB”, z-score -0.01802174 }, [1] { cohort “ACC”, expression_log2 2.725785, gene “CD274”, geneID 29126, protocol “RSEM”, sample_type…

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…

Information on “sample_name.cnt” obtained by an RSEM analysis 1 Hello, I obtained a “sample_name.cnt” in a newly created “sample_name.stat” directory after an RSEM-1.3.3 analysis. Shown below is the content of the “sample_name.cnt”. What do these numbers mean? Thank you in advance for your kindness. 0 2726098 0 2726098 1534055 1192043…

RSEM calculate-expression has only one sample in .isoforms.results file 1 Hello, I think I have a few misunderstandings about how to use RSEM, and have provided my script below. I have three questions: My script outputted a .isoform.results file, but with only one sample in it. As you can see…

Question about RNA-Seq data alignment 3 Hi, I have a question about genome alignment. I am working with RNA-Seq dataset to study the impact of Liquid Culture in response to virus of different doses in Human. I was exploring what could be the good strategy or best in practice method…

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…

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…

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…

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…

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…

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,…

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…

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…

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…

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

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…

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…

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…

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 …

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…

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…

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…

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…

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…

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…

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…

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….