Teaching. “Usus artium magister, dicendo dicere discunt.” (Eucharium Eyering, Copiae Proverbium)
Monatsarchiv für June 2019
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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