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Custome database creation from RNAseq dataset for proteomics database search help needed

I am not well experienced in custom database creation from RNAseq data for proteomics data analysis. I have RNAseq data and I was wondering if there is a software of pipeline which I can use to construct a database from these RNAseq data. Any help will be highly appreciated. I am looking for a workflow/software to do this

sequencing rna-seq
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updated by N15 N15 • written by javanokendo • javanokendo

1 answer

You need to assemble the transcriptome, and then translate into amino acid space. This can then be used as the fasta database you search against to assign PSMs.

Trinity is one of the top performing assemblers, perhaps you should give it a try:

https://github.com/trinityrnaseq/trinityrnaseq/wiki

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written by N15 N15

I have done the alignment with the star aligner and I got my BAM files sorted by coordinates.

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written by javanokendo • javanokendo

Thanks this worked for me and I really appreciate it

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written by javanokendo • javanokendo

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