Does Bedtools Intersect -V Consider Unmapped Reads "As Not In B"
bedtools intersect -v -abam my.bam -b myregions.gff > notinmyregions.bam
would we see reads with 4 in the FLAG field - i.e. unmapped reads in notinmyregions.bam
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I dont think so, you could always pipe in unmapped reads only to bedtools and see if there are any results:
samtools view -f 0x04 –b my.bam | intersectBed –abam stdin -b myregions.gff > notinmyregions.bam
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