Dear all, i need help in finding ssr from my rnaseq data. I already download the MISA program but have difficulities in executing it. can anybody teach me how to run it? anybody have the tutorial? thank you
Dear Hasyyati,
I can help you with the MISA program but before that u need to confirm weather MISA works with RNA sequences or not, because if go to the download page of MISA tool, and check requirements to run MISA their it is mentioned as DNA sequence in fasta format is required.
Dear Hasyyati Shabrina :
Alternatively, you may use PHOBOS Software (http://www.ruhr-uni-bochum.de/ecoevo/cm/cm_phobos.htm) to identify SSR sequences from your RNASeq data. Since you are from IPB, you may come to my lab (PMB Lab., Department of Agronomy and Horticulture, IPB) and I can show you how to run the PHOBOS Software and identify the SSR from your sequence data.
I would also suggest you take a look at our paper describing the use of PHOBOS to identify SSR sequences and use them to study genetic diversity of sago palm .
(https://www.jstage.jst.go.jp/article/jsbbs/advpub/0/advpub_18061/_article/-char/en)
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