Question

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

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4.5 years ago

javanokendo ▴ 60

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 • 985 views

ADD COMMENT • link updated 4.5 years ago by N15 ▴ 160 • written 4.5 years ago by javanokendo ▴ 60

score 3 · Accepted Answer · 2020-05-07

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4.5 years ago

N15 ▴ 160

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

ADD COMMENT • link 4.5 years ago by N15 ▴ 160

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