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oxydeepu 04-12-2013 12:22 AM

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,

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,

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

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?


NicoBxl 04-12-2013 02:13 AM

yes, check the IGV manual to have more infos :

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