Tag: readDNAStringSet

Query regarding phyloseq object construct with QIIME output 0 @6d5973d2 Last seen 15 hours ago India I used qiime pipeline to analyze 16s amplicon sequencing data now I want to take those outputs into r studio with the help of phyloseq package and want to create phyloseq object that’s how…

R is a very flexible programming language, and it allows developers to create their own data structures (called classes) for their packages. Over the years, some packages have become so popular that the classes they use to store data are now used the “standard” representations for particular types of data….

In R, I have a fasta (ex: Andrenidae.FASTA) with a few hundred nucleotide sequences from a dozen species. I want to get 1 consensus sequence for each species. Each sequence is made up of A/C/T/G/N, with N representing unknown nucleotides, and the sequence names are species names. All sequences are…

I am trying to replicate MEGA (models/find best DNA protein models) using R. After reading R AICs and BIC documentation I can’t understand how I can implement it. How can I implement AICs and BICs without having to especify the number of sequences in the fasta file (in case that…

I am trying to read a fastq-file with readDNAStringSet and having quite some trouble doing so. I need the names, aswell as the quality-scores. Right now I am using: readDNAStringSet(myFastqFile, format=”fastq”, use.names= TRUE, with.qualities = TRUE) But here i get the Error: “@” expected at beginning of line 1 I…

Trimming DNAStringSet 1 Hello, I am currently dealing with the problem of reading in a Fastq-File with “readDNAStringset”, trimming the Sequences and then writing them in to a new fastq-file. The reading of the fastq-file with “readDNAStringSet” is working just fine. I am then trying to trim a fixed length…