Question: Tophat2 And Bowtie2
0
gravatar for zhangpeng1334880
6.0 years ago by
shanghai
zhangpeng13348800 wrote:

I have a question about tophat2 and bowtie2. I want to align RNA-seq sequencing reads to reference sequences. My command is like this:
bowtie2:

bowtie2 -x genome Brm5.fastq -S Brm5.sam

tophat2:

tophat2 -G genes.gtf -o Brm5_thout genome Brm5.fastq

The read alignment rate of bowtie2 is 45.51%,while tophat2 is only 29.7%. So I am confused. All the data are the same,the tophat2 's result shoud be better than bowtie2 in the theory. Why is this happened, did I set wrong parameters in tophat2?Have anyone meet this kind question.

Any reply will be thankful.

bowtie2 tophat2 • 4.7k views
ADD COMMENTlink written 6.0 years ago by zhangpeng13348800
1

There are many parameters that you need to pass on in Tophat2.

For instance: are your reads mate-paired/paired end? length of your reads...

Here is a list of parameters in tophat that you can play with... This can significantly increase your percentage!

ADD REPLYlink modified 6.0 years ago • written 6.0 years ago by k.nirmalraman1000

Thanks a lot. I will try it.

ADD REPLYlink written 6.0 years ago by zhangpeng13348800

Dear k.nirmalraman, I have read the tophat manual carefully. And I have tried some protocol, like run without "-G genes.gtf", but it does not work. By the way, I am imitating the single_ended analysis in this literature http://www.ncbi.nlm.nih.gov/pubmed/22383036 . The specific data is at the bottom of page 565. And my reads length is 76. Do you have any ideas?

ADD REPLYlink written 6.0 years ago by zhangpeng13348800

could you pls now share your updated tophat command?

ADD REPLYlink written 6.0 years ago by k.nirmalraman1000
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