Question: How is Tophat producing more alignments than input reads?
gravatar for colin.kern
5.0 years ago by
United States
colin.kern920 wrote:

I'm running Tophat on paired end reads which I've run through Trimmomatic, so the command is something like:

tophat R1.paired.fastq.gz,R1.unpaired.fastq.gz,R2.unpaired.fastq.gz R2.paired.fastq.gz

If I count the reads in all four of those files and compare it with the number in the first line output from "samtools flagstat accepted_hits.bam" after running Tophat, the number in the flagstat output is higher than the number of total reads. From my understanding, that first number will only count a read once and any duplicate alignments will be counted in the "Secondary" number in the flagstat output. So how is this number higher than the number of reads input?

rna-seq samtools tophat • 1.2k views
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