Hi all,
I am trying to assemble 454 reads by aligning them to reference genome.
I have tried the official gsMapper before, which just gave me exon sequences, rather than transcripts sequences. Now, I am using BWA-SW to align the reads, and Cufflinks/Scripture to reconstruct the transcripts. Still, I can only get the individual exon sequences, instead of expected transcript sequences.
It seems the problem here is that BWA-SW is not a spliced aligner so that the splicing junction reads will be lost during the alignment. A spliced aligner, Tophat, is used in the tutorial of both Cufflinks and Scripture. However, this aligner is based on Bowtie, an aligner designed for short reads only.
Could anyone give me some suggestion of the spliced aligner suitable for 454 reads? I think BLAT would be an option, but still want to test some other methods developed recently.
Thanks,
Shuli
I am trying to assemble 454 reads by aligning them to reference genome.
I have tried the official gsMapper before, which just gave me exon sequences, rather than transcripts sequences. Now, I am using BWA-SW to align the reads, and Cufflinks/Scripture to reconstruct the transcripts. Still, I can only get the individual exon sequences, instead of expected transcript sequences.
It seems the problem here is that BWA-SW is not a spliced aligner so that the splicing junction reads will be lost during the alignment. A spliced aligner, Tophat, is used in the tutorial of both Cufflinks and Scripture. However, this aligner is based on Bowtie, an aligner designed for short reads only.
Could anyone give me some suggestion of the spliced aligner suitable for 454 reads? I think BLAT would be an option, but still want to test some other methods developed recently.
Thanks,
Shuli
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