Tag: GRCm39

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