Bowtie and Human transcripts

[MerFer]

Hallo Bowtie user,

I have a dateset with all transcripts from human genome. On the other side I have a set of RNA-seq reads (mate pairs/Illumina).
I would like to map these reads against the transcripts. .

I was thinking of using bowtie to accomplish this task, but I am not
very sure about which options or flags I should use. I thought, I have to map my reads using the bowtie option -norc. I have already tried this,
but I am not sure, if It is the rigth one.
Do you think, that these are the wrigth options to run bowtie for this task?
Thanks in advance
Mary

[bioinfosm]

Check out tophat, that uses bowtie for rna seq reads. Maybe you can find the flags and parameters for bowtie from tophat manual

[Ben Langmead]

Check out tophat, that uses bowtie for rna seq reads. Maybe you can find the flags and parameters for bowtie from tophat manual

I second that. Take a look at TopHat.

Thanks,
Ben

[MerFer]

Thanks for the answers.
The problem is that I dont want to map my reads against the whole genome,but I want to map them only against the transcript sequences (which contain already both sense and antisense transcripts). So I have already have the splice junctions in my transripts.
But I am not sure, if I should allow the bowtie to reverse my transcript sequences or not and how to handle the mate-pairs?
Thanks

[rkk]

Hi Merfer,

I am also in your situation I want to quantify the gene expression. How to do that? Where did you get the human genome transcripts? please suggest me.

Thanks in advance,