Hello,
Given X total reads in a FASTQ file, when the reads are aligned (by TopHat), there are greater than X reads mapped in the BAM file (according to samtools flagstats). How can this be?
In flagstats, is a single read counted more than once if it maps to more than one location?
Thanks,
Danielle
Given X total reads in a FASTQ file, when the reads are aligned (by TopHat), there are greater than X reads mapped in the BAM file (according to samtools flagstats). How can this be?
In flagstats, is a single read counted more than once if it maps to more than one location?
Thanks,
Danielle
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