Question: Custome database creation from RNAseq dataset for proteomics database search help needed
0
gravatar for javanokendo
17 days ago by
University of Cape Town
javanokendo0 wrote:

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 • 85 views
ADD COMMENTlink modified 17 days ago by NRC120 • written 17 days ago by javanokendo0
3
gravatar for NRC
17 days ago by
NRC120
NRC120 wrote:

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 COMMENTlink written 17 days ago by NRC120

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

ADD REPLYlink written 17 days ago by javanokendo0

Thanks this worked for me and I really appreciate it

ADD REPLYlink written 16 days ago by javanokendo0
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