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compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
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question about databases from RNASeq data #277

Closed fazeliniah closed 7 years ago

fazeliniah commented 7 years ago

Hi, My question is about generating protein/peptide databases from RNA-Seq data. I would like to know what tools you recommend for processing RNA-Seq data to generate fasta databases for the Searchgui. In particular, I am interested in 6 reading frame translation for short RNA reads. Thanks H

mvaudel commented 7 years ago

Hi,

I think customProDB is the reference tool to create databases from RNA-Seq data. I am not sure in the particular case of short reads. We don't develop such tools ourselves I am afraid. https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btt543

SearchGUI and PeptideShaker will accept databases in most formats, but in case you are using a custom format, you might need to reformat your fasta file. You will find a generic format in our help below. https://github.com/compomics/searchgui/wiki/DatabaseHelp

Hope this helps,

Marc