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

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.

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

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

WHat about the second question?

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

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

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