Different Results Of Tophat And Bowtie2

Question

[Mohammad Reza Bakhtiarizadeh]

I am trying to map RNASeq paired reads (60bp) (breast cancer) to human genome (without mt genome) using Tophat (v2.0.10) and I am returning an alignment rate of 64%. tophat -p 8 -r 200 --mate-std-dev 50 --b2-very-sensitive --phred64-quals -g 10 --microexon-search -G Homo_sapiens.GRCh37.74.gtf GRCh37.74 ff1.fastq ff2.fastq

I used the same reads in Bowtie version 2.1.0 and returned an alignment rate of 79.58% bowtie2 -p 8 --phred64 --very-sensitive -x GRCh37.74 -1 ff1.fastq -2 ff2.fastq -S out.sam

I checked my reads with fastqc and they are ok. but my problem is that why results of tophat and bowtie2 are different? I am really confused. if possible help me.

Thanks in advance

[Parham]

Shouldn't bowtie2 be ran with TopHat together?!

Answer 1

[Charles Warden]

It looks like you are providing a lot more parameters to TopHat. What happens if you run TopHat (or Bowtie) with just the default parameters?

[Mohammad Reza Bakhtiarizadeh]

Thanks for your answer, but I try it and get a sane results. I really don't know what is the problem :(