Tag: readDNAStringSet

r – Displaying BIC and AICs from MSA nucleotide multisequence fasta file

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…

Continue Reading r – Displaying BIC and AICs from MSA nucleotide multisequence fasta file

error reading fastq-files with readDNAStringset

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…

Continue Reading error reading fastq-files with readDNAStringset

Trimming DNAStringSet

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…

Continue Reading Trimming DNAStringSet