SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
cuffdiff for differential gene testing Paul Walker RNA Sequencing 4 01-26-2015 08:04 AM
how do you find a possible intron on a gene? bbsinfo Illumina/Solexa 2 12-30-2011 10:05 AM
How to find closet gene koneru_18 Bioinformatics 5 10-14-2011 03:43 AM
help with differential gene expression with cufflinks and tophat waterboy Bioinformatics 1 11-28-2010 09:51 AM
Differential gene expression of gene clusters anjana.vr RNA Sequencing 1 10-28-2010 10:33 AM

Reply
 
Thread Tools
Old 04-02-2012, 06:12 AM   #1
Fedster
Junior Member
 
Location: London

Join Date: Mar 2012
Posts: 5
Default using tophat to find differential splices of ONE gene

I have the CEU RNA seq fastq data from here

http://jungle.unige.ch/rnaseq_CEU60/

I would like to use tophat to see if I can find more than one splice variants for one gene (actually two, the two genes are quite similar, but on different chromosomes).

I have a nice small fasta file with a number of possible predicted splice variants for the gene(s); I also have the hg18 index sequence for bowtie.

It is not quite clear to me what's the correct step now:

tophat /path/to/h_sapiens reads1.fq,reads2.fq,reads3.fq

does suspiciously look like it will happily ignore the fact I only care for one gene, rather than the whole hg18 genome.

I am on a cluster, so I cannot be interactive and I cannot test stuff easily just by trying (and I'm running out of disk space!). How do I tell tophat to just align stuff to my gene in the small fasta file? do I have to run bowtie on the fasta file first somehow?
Fedster is offline   Reply With Quote
Old 04-02-2012, 03:46 PM   #2
sjm
Member
 
Location: St Louis, MO

Join Date: Nov 2009
Posts: 27
Default

I think as a first step, you will indeed need to have bowtie build a database from your fasta file.

bowtie-build /path/to/fasta name_of_database

Then have tophat align your reads to that database:

tophat name_of_database reads1.fq,reads2.fq (etc.)
sjm is offline   Reply With Quote
Reply

Tags
alignment, bowtie, differential splicing, rnaseq, tophat

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:22 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO