RNA-seq assembly and reference genome

lfaino · 04-13-2011, 04:12 AM

Dear community,
I have a question.
I have an RNA-seq by Illumina pair ends. I have a reference genome and transcriptome. My question is if there is any software that I can use to map the RNA-seq reads on the reference transcriptome and retrieve the assembled transcriptome based on my sequences. I want this because my coverage is low and in this way I can use a known reference to get better information about my transcriptome too.

Regards
Luigi

harrike · 04-13-2011, 05:34 AM

commercial software: CLC genome workbench. www.clcbio.com. It is quite expensive.

There are many free software shared in this community. You'd better use "search" to get what you want.

Thorondor · 04-13-2011, 05:57 AM

actually it is not that easy, there are many assemblers around but they mostly require a genome as reference and not a transcriptome. I also checked for assemblers where you can give a transcriptome of a near relative as reference but didn't found anything. :-(

You maybe can "fake" the transcriptome as genome, but I don't know if this will work.

If you want to use your genome as reference you could try cufflinks.

ksc · 04-13-2011, 08:05 AM

I am using BWA to remap mRNAseq data to a reference transcriptome and samtools to call the consensus of the remapped transcriptome. I have also used CLC for this purpose, as suggested by harrike. I have not yet used paired-end data, but I believe both packages can handle paired-end data.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Targeted Genome Assembly for region poorly represented in reference genome?	gumbos	Bioinformatics	1	01-09-2012 05:01 PM
RNA-Seq: Full-length transcriptome assembly from RNA-Seq data without a reference gen	Newsbot!	Literature Watch	7	10-26-2011 06:37 AM
reference based RNA-seq assembly	explorebio	RNA Sequencing	0	04-29-2011 02:08 AM
Anyone with Solexa RNA-seq 150+bp for non-model sps with no close reference genome?	avilella	RNA Sequencing	0	03-20-2010 04:46 AM
Anyone with Solexa RNA-seq 75+bp for non-model sps with no close reference genome?	avilella	RNA Sequencing	0	01-13-2010 03:46 AM

04-13-2011, 04:12 AM	#1
lfaino Junior Member Location: ITA Join Date: Mar 2011 Posts: 9	RNA-seq assembly and reference genome Dear community, I have a question. I have an RNA-seq by Illumina pair ends. I have a reference genome and transcriptome. My question is if there is any software that I can use to map the RNA-seq reads on the reference transcriptome and retrieve the assembled transcriptome based on my sequences. I want this because my coverage is low and in this way I can use a known reference to get better information about my transcriptome too. Regards Luigi

04-13-2011, 05:34 AM	#2
harrike Member Location: St. Louis, MO Join Date: Jun 2010 Posts: 29	commercial software: CLC genome workbench. www.clcbio.com. It is quite expensive. There are many free software shared in this community. You'd better use "search" to get what you want.

04-13-2011, 05:57 AM	#3
Thorondor Member Location: Heidelberg Join Date: Feb 2011 Posts: 69	actually it is not that easy, there are many assemblers around but they mostly require a genome as reference and not a transcriptome. I also checked for assemblers where you can give a transcriptome of a near relative as reference but didn't found anything. :-( You maybe can "fake" the transcriptome as genome, but I don't know if this will work. If you want to use your genome as reference you could try cufflinks.

04-13-2011, 08:05 AM	#4
ksc Junior Member Location: St. Louis, MO Join Date: Apr 2011 Posts: 4	I am using BWA to remap mRNAseq data to a reference transcriptome and samtools to call the consensus of the remapped transcriptome. I have also used CLC for this purpose, as suggested by harrike. I have not yet used paired-end data, but I believe both packages can handle paired-end data.