Question: How many reads used by a assembler for transcriptome assembly
0
gravatar for seta
3.3 years ago by
seta1.1k
Sweden
seta1.1k wrote:

Hi all,

I would like to know how many reads used by the assemblers, like Trinity and Soap-denovo trans tools for making a de novo transcriptome assembly? Mapping read back to the assembly is the right option?, I usually run bowtie2 with default commands. Could you please put the important options to use the right command?

Thanks for sharing what you want.

ADD COMMENTlink modified 3.3 years ago by Antonio R. Franco4.0k • written 3.3 years ago by seta1.1k
0
gravatar for Antonio R. Franco
3.3 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.0k wrote:

I would say as many reads as possible. You can even mix the reads from different experiments

In the absence of a nice annotated reference genome, mapping to a transcriptome is perfectly valid

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by Antonio R. Franco4.0k
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