Visualing the alignment on a genome without annotations

oxydeepu · 04-12-2013, 12:22 AM

Hi All,

I'm working in a lab which uses planaria as a model organism, which have a contig level of genome assembly. I have RNA-Seq data from the same. Now I am trying to visualize the alignment of the reads on the genome. I also want to visualize the transcripts made from the cufflinks assembly of those RNA-Seq reads. The problem is RNA-Seq alignment is using bowtie and Cufflinks transcripts are using blast. Can anyone help me in visualizing the same. I just want to validate that the transcripts alignment on the genome corresponds to the RNA-Seq alignment. Please help. Thank you in advance.

Best Regards,
Deepak

NicoBxl · 04-12-2013, 01:16 AM

I you have a bam file from an aligner (you used bowtie, but you should use a splice-aware aligner like tophat or STAR) and a gtf (or gff) from cufflinks, you can use IGV to visualize the alignment and check the annotation created by cufflinks.

oxydeepu · 04-12-2013, 01:26 AM

Thank You Nico,

I will definitely try the suggestion. One doubt, does IGV, inputs a genome fasta file or does it have a built in database for genomes? What If I want to put in the EST alignment information, which is a blast?.

Thank you for your time once again.
Best Regards,
Deepak

NicoBxl · 04-12-2013, 01:28 AM

IGV has several genomes in its database, but it accept also fasta files.

oxydeepu · 04-12-2013, 01:41 AM

WHat about the second question?

NicoBxl · 04-12-2013, 01:42 AM

you should convert your blast output to gff. Check here http://www.biostars.org/p/277/

oxydeepu · 04-12-2013, 01:52 AM

So now I can include this gff also to the IGV viewer and visualise. So does this take care of the exon informations, any clue about that?

Thanks,
Deepak

NicoBxl · 04-12-2013, 02:13 AM

yes, check the IGV manual to have more infos : http://www.broadinstitute.org/igv/

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04-12-2013, 12:22 AM	#1
oxydeepu Member Location: bangalore,india Join Date: Jul 2011 Posts: 41	Visualing the alignment on a genome without annotations Hi All, I'm working in a lab which uses planaria as a model organism, which have a contig level of genome assembly. I have RNA-Seq data from the same. Now I am trying to visualize the alignment of the reads on the genome. I also want to visualize the transcripts made from the cufflinks assembly of those RNA-Seq reads. The problem is RNA-Seq alignment is using bowtie and Cufflinks transcripts are using blast. Can anyone help me in visualizing the same. I just want to validate that the transcripts alignment on the genome corresponds to the RNA-Seq alignment. Please help. Thank you in advance. Best Regards, Deepak

04-12-2013, 01:16 AM	#2
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	I you have a bam file from an aligner (you used bowtie, but you should use a splice-aware aligner like tophat or STAR) and a gtf (or gff) from cufflinks, you can use IGV to visualize the alignment and check the annotation created by cufflinks.

04-12-2013, 01:26 AM	#3
oxydeepu Member Location: bangalore,india Join Date: Jul 2011 Posts: 41	Thank You Nico, I will definitely try the suggestion. One doubt, does IGV, inputs a genome fasta file or does it have a built in database for genomes? What If I want to put in the EST alignment information, which is a blast?. Thank you for your time once again. Best Regards, Deepak

04-12-2013, 01:28 AM	#4
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	IGV has several genomes in its database, but it accept also fasta files.

04-12-2013, 01:41 AM	#5
oxydeepu Member Location: bangalore,india Join Date: Jul 2011 Posts: 41	WHat about the second question?

04-12-2013, 01:42 AM	#6
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	you should convert your blast output to gff. Check here http://www.biostars.org/p/277/

04-12-2013, 01:52 AM	#7
oxydeepu Member Location: bangalore,india Join Date: Jul 2011 Posts: 41	So now I can include this gff also to the IGV viewer and visualise. So does this take care of the exon informations, any clue about that? Thanks, Deepak

04-12-2013, 02:13 AM	#8
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	yes, check the IGV manual to have more infos : http://www.broadinstitute.org/igv/