Michael Grünstäudl (Gruenstaeudl), PhD

Postdoctoral Researcher at the Freie Universität Berlin

Monatsarchiv für June 2019

Teaching in Spring 2019

Teaching. “Usus artium magister, dicendo dicere discunt.” (Eucharium Eyering, Copiae Proverbium)                

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Extracting mapped R1 and R2 reads from SAM file

Extracting those that mapped Recently, I found myself in need of extracting only those reads from a sequence alignment map (SAM) file that actually mapped to the reference genome, while maintaining the separation into the paired-end read design. By using a combination of samtools, bedtools and awk, this can be done very efficiently: INFL=MySamples.sam STEM=${INF%.sam*} […]

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