Tag: GRCm39

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…