Tag: RSeQC

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…

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[MonashBioinformaticsPlatform/RSeQC] junction_saturation not suit for bam/sam file generated by minimap or pbmm2

because the CIGAR in bam/sam file generated by minimap2 contain “=” , represent right match with reference, and “X”, represent wrong match with reference. while the bam_cigar.py in ./lib/qcmodule/bam_cigar.py only suit for bam/sam generated such as BWA/bowtie, which CIGAR contain only “M” ,represent mis/match. So i modified the bam_cigar.py 77…

Continue Reading [MonashBioinformaticsPlatform/RSeQC] junction_saturation not suit for bam/sam file generated by minimap or pbmm2

Highly mapped to introns

Highly mapped to introns 0 Hi, I am analyzing RNA-seq data from human blood samples. I checked the read distribution using RSeQC read_distribution after mapping by STAR. Usually, I get more than 80% of reads mapped to exons. However, at this time, the result showed only several % were mapped…

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Interpreting read coverage over gene body plot

Interpreting read coverage over gene body plot 0 Hi, I’m working on some RNA-seq data for my thesis and I was hoping that someone could help me out. My sequencing library was prepared using Illumina TruSeq Stranded mRNA kit and sequenced with a NovaSeq sequencer. After read alignment I did…

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