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11.0 years ago
zhangpeng1334880
•
0
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.
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!
Thanks a lot. I will try it.
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?
could you pls now share your updated tophat command?