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How many reads used by a assembler for transcriptome assembly

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.

transcriptome-assembly rna-seq
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updated by Ram Ram • written by seta seta

1 answer

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

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written by Antonio R. Franco Antonio R. Franco

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