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

Question

[javanokendo]

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

Answer 1

[N15]

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

[javanokendo]

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

[javanokendo]

Thanks this worked for me and I really appreciate it