Question: How is Tophat producing more alignments than input reads?
0
gravatar for colin.kern
4.2 years ago by
colin.kern750
United States
colin.kern750 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 • 1.1k views
ADD COMMENTlink written 4.2 years ago by colin.kern750
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1758 users visited in the last hour