Tag: GRCm39

This is probably a duplicated question from: How To Convert Bed Format To Gtf? How to convert original BED file to a GTF ? Converting different annotation file formats (GTF/GFF/BED) to each other How to change scaffold.fasta file or scaffold.bed file to GTF file? Convert bed12 to GFF convert bed12…

featureCounts error??? 0 # get gtf # wget #https://ftp.ensembl.org/pub/release-110/gtf/mus_musculus/Mus_musculus.GRCm39.110.gtf.gz input.dir <- “/home/laudy/data/featurecounts/” setwd(input.dir) featureCounts -p -O -T -a /input.dir/Mus_musculus.GRCm39.110.gtf -o /input.dir/quants.txt /input.dir/PMN_CTRAligned.sortedByCoord.RD.RG.RC.out.bam please can someone tell me what’s wrong Im tried allllllll the options and he give me the same error: Error: object ‘p’ not found or Error: unexpected symbol…

Hi all! Introducing the Non-Overlapping Exon Length calculator (NOEL), an extremely fast GTF/GFF per gene exon length extractor written in Rust. See the code and latest updates here: github/alejandrogzi/noel In case you do not want to read the whole text: NOEL outperforms all open-sourced scripts/tools for this task. It can…

Hi everyone, I hope you’re doing well. I’ve been encountering a puzzling issue in my RNA-seq analysis pipeline and was hoping to get some insights from this knowledgeable community. I’m currently working on an RNA-seq project, where I’ve aligned my trimmed reads to the mouse reference genome (GRCm39) using HISAT2…

I generated a new transgenic mouse through random multi-copy integration of a 10.316 Kb DNA fragment with a known sequence . We performed WGS using the PromethION flow cell. From the core I received 500+ fastq files that I have subsequently merged. So far I have performed: de novo assembly…

Introduction Single-cell RNA sequencing (RNA-seq) was first achieved by using a quantitative cDNA amplification method and applied to mouse oocytes (Kurimoto et al, 2006; Tang et al, 2009). It has since provided unprecedented opportunities for the study of cellular differentiations, states, and diseases in various biological fields, including developmental biology,…

Gene-based differential expression analysis of genetically modified mouse line 0 Hello, I am trying to analyze my bulk RNAseq data set from hippocampal tissue extracted from our WT/KO mice. The knockout consists of a 10kb deletion in a single exon of our gene of interest. I want to look at…

Are there mm39/GRCm39 blacklist regions? 1 blacklist • 1.8k views • link updated 2 hours ago by igor 13k • written 15 months ago by Ian 6.0k Login before adding your answer. Traffic: 1681 users visited in the last hour Read more here: Source link

New mouse reference genome (GRCm39/mm39) 1 Hi, I am planning to perform sequencing alignment using the new mouse reference genome mm39 available on UCSC: hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/ (bowtie2 on chipseq data). Did I understand correctly that both mm39.2bit and mm39.fa.gz are the same and I can use either of them (2bit file…

Unusual pattern in heatmap from ChIP-seq 0 Hello! I am plotting some heatmaps for a certain histone mark from a ChIP-seq experiment. I am producing the heatmaps using both computeMatrix and plotHeatmap functions from deeptools. The coordinates regions used for computeMatrix are all coding regions for the mouse genome, sorted…

D942–D949 Nucleic Acids Research, 2023, Vol. 51, Database issue Published online 24 November 2022 doi.org/10.1093/nar/gkac1071 GENCODE: reference annotation for the human and mouse genomes in 2023 Adam Frankish 1,* , Sı́lvia Carbonell-Sala2 , Mark Diekhans 3 , Irwin Jungreis 4,5 , Jane E. Loveland 1 , Jonathan M. Mudge1 ,…

An important task of bulk rna-seq analysis is the different expression , which we can perform with omicverse. For different expression analysis, ov change the gene_id to gene_name of matrix first. When our dataset existed the batch effect, we can use the SizeFactors of DEseq2 to normalize it, and use…

Issues with running featureCounts with STAR 0 I am trying to generate a count table after aligning my CLIP-seq results to a genome index. I have been using several online tutorials, but I am running into an issue when using featureCounts from bioconda subread. I have tried referencing a folder…

doi: 10.1093/bioinformatics/btad198. Online ahead of print. Affiliations Expand Affiliations 1 Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA. 2 Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA. 3 Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill,…

The completion of the full “telomere-to-telomere” (T2T) human genome last year emphasized that genome sequences that were previously thought to be “complete” were not, in fact, complete at all.  Moreover, many recent genomes are sequenced with short-read sequencing technologies, which fragment DNA into short segments, typically 150-300 base pairs long,…

GetBM – GERP conservation score for GRCm39 2 Hi all, Ensembl has GERP scores for each of their mus musculus SNPs (for example: rs31948051 has a GERP score of -0.4). I’m trying to see if biomaRt (the getBM function) to get these scores, but it doesn’t seem to have any…

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…

Which reference transcriptome/genome to use for mus musculus if I know the particular strain involved in the experiment? 0 I know my samples are from C57BL6. Should I use the specific for C57BL6 or just generic mus musculus reference transcriptomes/genomes for alignments? I am worried that the file size for…

I am trying to index my reference genome using bwa-mem2 (latest version). I downloaded GRCm39.primary_assembly.genome.fa from www.gencodegenes.org/mouse/release_M27.html and run the following bwa-mem2-2.0pre2_x64-linux/bwa-mem2 index /media/jay/Data/reference_genome/GRCm39.primary_assembly.genome.fa I got this output [bwa_index] Pack FASTA… 7.03 sec init ticks = 216871092051 ref seq len = 5456444902 binary seq ticks = 176853625961 build index ticks…

Hello all, I checked the questions posted on the forum, but couldn’t find the answer I was looking for, so I’m leaving a question. I’m doing total RNA sequencing and have a question about my results. There are three types of data: from AML12, 3T3L1 and mouse testis. (All data…

HISAT2 paired end multiple files loop error 0 Hi, I got stuck with running hisat2 with a loop. my input files are here, here is my loop code, for f in `ls -1 *_1_fp.fastq.gz | sed ‘s/_1_fp.fastq.gz//’ ` do hisat2 -rna-strandness RF -x GRCm39 -1 ${f}_1_fp.fastq.gz -2 ${f}_2_rp.fastq.gz 2> ${f}.log|…

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]….

HI everyone. I have a set of mouse SNPs (~974) from GRCm39 that I’m trying to get either GERP or UCSC Conservation scores on. To do this, I’m using rtracklayer to try to query the ranges of the SNP and return the multiz35way conservation score. However, when I do this,…

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…

Get gene names from rs SNP ids for mmusculus_gene_ensembl 1 I have mouse data with an old mapping from rs SNP IDs to base pair position and chromosome. I would like to query Ensembl to get the genes and then the gene annotations for the rs SNP IDs in my…

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…

Hi everyone, first time working with mouse samples and unfortunately, there are fewer resources available for the latest mouse Ensembl genome than I was expecting. What I’ve done: I performed rRNA depletion on total RNA extracted from mouse tissue and created Illumina libraries using a cDNA synthesis kit with random…

Kallisto mapping paired end 0 Hello everyone, I am new to bioinformatics and i am trying to use kallisto to map paired end data. However, I got an error by running the command. So does anyone know what did I do wrong here? Thank you! Here is my command: kallisto…

Good or bad idea to annotate with newer genome build? 0 Hello Biostars Community, If the probe sequences on a mouse methylation beadchip array is based on the (mm10) GRCm38 genome build, would it be a bad idea to annotate the probes with the latest genome build (mm39) GRCm39? I…

MiRBase miRNA analysis with STAR 0 Hi All, I am using the latest mice reference genome (GRCm39) for small RNAseq/miRNA-seq analysis. MiRBase database doesn’t have any GFF/GTF file for the mouse mature-miRNA/loop-miRNA. I just have mature-miRNA and loop-miRNA fasta sequences from MiRBase. How I can use the STAR tool to…