Hi all,
I want to do rarefaction analysis for the plant "Juncus effusus" transcriptome assembly. At the moment I have Fasta file with final assembly. I wonder how can I use this dataset? Is there any tool available for this purpose? If there is no direct tool available, how can I get each gene abundance? an example file with a few reads is attached!
I think you have asked the wrong person as I have never worked in the field you are asking about
First you need to annotate your sequences to find out from which genes/functions each sequence belong. Then you can rarefy the gene count table directly, it is much more efficient, fast and as roubust to do it like this. Then you need to run proper statistical analysis to mine your data properly. Good luck :-)
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