Tag: GRCm39

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…

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

Get gene names from rs SNP ids for mmusculus_gene_ensembl

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…

Continue Reading Get gene names from rs SNP ids for mmusculus_gene_ensembl

Hisat2 – stringtie – deseq2 pipeline for bulk RNA seq

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…

Continue Reading Hisat2 – stringtie – deseq2 pipeline for bulk RNA seq

Low transcript quantification with Salmon using GRCm39 annotations

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…

Continue Reading Low transcript quantification with Salmon using GRCm39 annotations

Kallisto mapping paired end

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…

Continue Reading Kallisto mapping paired end

Good or bad idea to annotate with newer genome build?

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…

Continue Reading Good or bad idea to annotate with newer genome build?

MiRBase miRNA analysis with STAR

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…

Continue Reading MiRBase miRNA analysis with STAR