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Old 02-11-2015, 01:32 AM   #1
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Question aligning pre-assembled transcriptomes to genomes


I have been given a pre-assembled transcriptome for my organism, which was generated using de novo assembly of RNAseq reads, assembly or reads against a reference genome and by assembly of ESTs. Each method was run using several different assemblers and then the results were clustered to remove redundancy and further processed according to some criteria about reading frames to produce a final transcript set.

I now wish to align this transcript set against the reference genome, so I can view it together with the genome, for example using the IGB. What is the best tool to do this? I presume TopHat is sub-optimal, because it's designed for short reads, not full length transcripts? In addition, my transcript set is in FASTa format - and I think I'm right in saying that you can only run TopHat on FASTq files. I was looking at a tool called LAST - does anyone know if this is suitable?

Please be clear and simple in any answers - I'm an experimentalist learning how to analyse his own sequencing data!

Any help would be greatly appreciated.

Last edited by skeffington; 02-11-2015 at 02:03 AM.
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Old 02-11-2015, 02:32 AM   #2
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I've had good results with GMAP ( for such tasks.
Otherwise BLAT ( is a quite popular choice.
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Old 02-11-2015, 03:28 AM   #3
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I would also recommend BLAT.
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alignement, transcriptome

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