Hi all.
I have transcriptome data from 454 sequencer. I have assembled it using de novo gsAssembler and formed a contigs (i am not using isotigs). I want to find alternative splicing events from these contigs, so far i am doing BLAT search for each contig as reference genome is known for my organism. Analyzing BLAT output in genome browser of UCSC comparing my contigs alignments with known mRNA, EST sequences whether splicing is different form reported mRNA splicing.
Is it the right approach?
the problem is i have to go one by one contig, it is taking to much time. Is there any other approach to speed up finding alternative splicing.
Thanks
I have transcriptome data from 454 sequencer. I have assembled it using de novo gsAssembler and formed a contigs (i am not using isotigs). I want to find alternative splicing events from these contigs, so far i am doing BLAT search for each contig as reference genome is known for my organism. Analyzing BLAT output in genome browser of UCSC comparing my contigs alignments with known mRNA, EST sequences whether splicing is different form reported mRNA splicing.
Is it the right approach?
the problem is i have to go one by one contig, it is taking to much time. Is there any other approach to speed up finding alternative splicing.
Thanks
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