Question: How to pull out protein sequences from from BAM files containing genomic alignments
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gravatar for julia92796
17 months ago by
julia927960
julia927960 wrote:

Hi,

I'm trying to pull out protein sequences from BAM files containing genome alignments. What is the best way to do this? Right now, I have a BAM file containing the neanderthal alignment to the human genome and a fasta file containing the human reference sequence. I wasn't sure whether the next step would be to pull out the neanderthal consensus sequence using SAMtools. If so, where do I go from there, and if that's not the case, what should I do next?

ADD COMMENTlink written 17 months ago by julia927960

Have you seen this thread: Looking for neanderthal genomes to download

What are you looking to get at the end?

ADD REPLYlink written 17 months ago by genomax39k

Thanks, this thread is helpful. I have a list of human proteins, as well as the genes coding for these proteins, and I'm trying to find homologs to the proteins in humanoid species. I suspect that the next step in my process is generating the consensus sequence for the neanderthal genome, but after that, I'm not sure exactly where to proceed.

ADD REPLYlink written 17 months ago by julia927960
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