Hi all,
I'm running gsMapper with "-cdna -gref" options. I'm surprised to find the majority of the contigs assembled correspond to individual exons, rather than the transcripts!
A possible reason I can image is that there may be more then one isoform generated from the same locus, so that the assembler can't assemble the reads from this gene into one. However, this is not the scenario since we have separated isoforms before sequencing.
I have searched this problem but can't find any information. So I think this is probably not caused by the inability of gsMapper to detect introns. Any suggestion?
Thanks!
BTW, it's really strange that at least one transcript with several huge introns (> 3kb) has been assembled successfully, where many transcript with much short introns are failed to be assembled...
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