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Tophat2 And Bowtie2

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.

tophat2 bowtie2
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written by zhangpeng1334880 • zhangpeng1334880

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!

• 277 views • link
written by k.nirmalraman k.nirmalraman

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?

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written by zhangpeng1334880 • zhangpeng1334880

could you pls now share your updated tophat command?

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written by k.nirmalraman k.nirmalraman

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