I´m processing a fastq file of reads that have already paired. Trying to get the GC content i get this error ???
> fq <- readFastq(file) > fq class: ShortReadQ length: 50545 reads; width: 79..503 cycles > gc <- gcContent(fq) Warning messages: 1: In if (nbins > .Machine$integer.max) stop("attempt to make a table with >= 2^31 elements") : the condition has length > 1 and only the first element will be used 2: In if (is.na(nbins)) stop("invalid value of 'nbins'") : the condition has length > 1 and only the first element will be used
Looking at the fastqfile
> qual <- as(quality(fq), "matrix") > qual [,501] [,502] [,503] [1,] NA NA NA [2,] NA NA NA
I´ve noticed that the qual object contains NA values at the end of the sequence. Any idea ??
I have merged pairs using bbmerge first but don´t see any problem in the fastq file. I have tried other programs and fastq file look ok.