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
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