Tag: samtool

Filteration of uniquely mapped reads

Filteration of uniquely mapped reads 2 Hello I have BAM-full file with reads mapped to “human and mouse” chromosome file. Now I would like to extract reads mapped only to “mouse” (means not mapped to human chromosome”. This is the protocol I am using : From BAM-full, extract reads mapped…

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[SOLVED] changing the order of input changes samtools merge ouput

I realized that this is a stupid mistake I have made. Since samtools do not overwrite the files by default, the output that I get from samtools merge output.bam f2.bam f1.bam wan’t what I thought it was below is my original post ++++++++++++++++++++++++++ I’m using samtool/1.9.0 and I’m trying to…

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Disappearing CB, the bam tag after samtools sort -t CB

  I’ve been trying to setup an analysis pipline for RNAvelocity in AWS EC2. I used one of the 10x dataset, 10k Peripheral blood mononuclear cells (PBMCs) from a healthy donor, Single Indexed, as a test model to setup the pipeline. For speed and cost saving, I first used samtools…

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