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degregory / SAM_Refiner

Program for gathering variant information from a SAM formated file.
GNU General Public License v3.0
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Amino acid fasta file #5

Closed kayobianco closed 1 year ago

kayobianco commented 1 year ago

Hello, Is it possible to save the fasta file of amino acid sequences annotated as Sc2?

Best regards, Kayo

degregory commented 1 year ago

Could you clarify what you are asking? SAM Refiner uses SAM files as input and outputs tsv files. Any fasta files would be upstream and would be nucleotide sequences, not amino acid. What is Sc2 in this context?

kayobianco commented 1 year ago

Dear degregory, Sorry if my question wasn't clear.

Can SAM_refiner save fasta file of nucleotides paired with SARS-CoV-2 (Sc2) reference sequence?

degregory commented 1 year ago

I think I understand what you are wanting. It won't output a fasta, but if you have it output the read tsv ( --read 1 ), it will preserve the labels from the fasta/fastq you are processing, making it easier to link the SAM Refiner output with the nt sequence. Hope that will let you get to what you want.