Reading FASTA file with multiple sequences
Hello all,
I'm trying to read a fasta file that has over 5000 sequences. The plan is to create a vector that calls out all the sequences, and those sequences I'll carry over to Bio Linux after I turn them into protein. I've done this, but with only one sequence at a time (that and I'm still new to RStudio). Please see below for the codes I'm using... Can someone please tell me where I'm going wrong?
contigs= read.fasta("contigs.fasta", seqtype = “DNA”)
contigs_dna= contigs[[1]] (I think this is the part where things go wrong. I'm not sure what code to use in order for the program to recognize the 5000+ sequences.)
getTrans(contigs_dna, sens = "F", NAstring = "X", ambiguous = FALSE, frame = 0, numcode = 1)
contigs_aa= getTrans(contigs_dna,sens = "F")
write.fasta(contigs_aa,contigs_aa,file.out = "contigs_aa.fasta")
contigsaafile = read.fasta("contigs_aa.fasta", seqtype = "AA")
getAnnot(contigsaafile)
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Hello Seot!
It appears that your post has been cross-posted to another site: https://support.bioconductor.org/p/92193/
This is typically not recommended as it runs the risk of annoying people in both communities.