Question: Different Results Of Tophat And Bowtie2
gravatar for Mohammad Reza Bakhtiarizadeh
5.6 years ago by
Tehran university

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

ADD COMMENTlink modified 5.6 years ago by Neilfws48k • written 5.6 years ago by Mohammad Reza Bakhtiarizadeh290

Shouldn't bowtie2 be ran with TopHat together?!

ADD REPLYlink written 4.9 years ago by Parham1.4k
gravatar for Charles Warden
5.6 years ago by
Charles Warden7.2k
Duarte, CA
Charles Warden7.2k wrote:

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?

ADD COMMENTlink written 5.6 years ago by Charles Warden7.2k

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

ADD REPLYlink written 5.6 years ago by Mohammad Reza Bakhtiarizadeh290
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