Hi All,
I want to use comparative-based assembler for short-reads for assembling mRNA-seq. For example, if we have human tissue mRNA short-reads, we want to reassemble the short-reads into transcripts by comparing with human genome, which software is more suitable for this task?
I found AMOScmp-shortreads might be useful for this purpose, but when I read the manual, I found AMOScmp do not support fastq format. I also don't know the performance for this software.
In further, do anyone compare the performance of de novo based assembler with reference-based assembler for mRNA-seq?
Thanks,
ZCH
I want to use comparative-based assembler for short-reads for assembling mRNA-seq. For example, if we have human tissue mRNA short-reads, we want to reassemble the short-reads into transcripts by comparing with human genome, which software is more suitable for this task?
I found AMOScmp-shortreads might be useful for this purpose, but when I read the manual, I found AMOScmp do not support fastq format. I also don't know the performance for this software.
In further, do anyone compare the performance of de novo based assembler with reference-based assembler for mRNA-seq?
Thanks,
ZCH
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