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Old 07-14-2012, 11:52 AM   #1
BenLerch
Junior Member
 
Location: Portland, Or

Join Date: Jun 2012
Posts: 1
Default Tophat/Bowtie2 inconsistency in number of paired reads

Hi all,
I find when I align using bowtie2 all of my reads are paired, and when I align using tophat none of my reads are paired:
Bowtie2 output: 67680344 reads; of these:
67680344 (100.00%) were paired...
Tophat output: 67609802 reads; of these:
67609802 (100.00%) were unpaired...
here is my bowtie2 command:
bowtie2 -p 10 GenomeName -S OutputFilePath -1 R1.fastq -2 R2.fastq
here is my tophat command:
tophat -p 10 -G genes.gtf -o OutputFilePath GenomeName R1.fastq R2.fastq

Does anyone know how to explain the discrepancy?

-Ben
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bowtie, bowtie2, rna-seq, tophat, tophat 2.0.4

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