When trying to use ATACseqQC on a larger bamfile, I receive the following error:
Error in .local(x, ...) : strand values must be in '+' '-' '*' Calls: splitGAlignmentsByCut ... normalizestrandreplacement_value -> strand -> strand -> .local
I checked the structure of the bamfile using str(gal) and under strand values I see: Factor w/ 3 levels "+","-","*": 3.
The bamfile is available to be downloaded here: http://s3.amazonaws.com/mudaser/bamfiles/112R-rep1-chr1-bwa.bam
The R script is available to be downloaded here: http://s3.amazonaws.com/mudaser/bamfiles/ATACseq_heatmap.R
The log file that shows the full error is available to be downloaded here: http://s3.amazonaws.com/mudaser/bamfiles/Heatmap.log
Any insight would be much appreciated.
(Ideally, I would like to use the entire bamfile without limiting to chr1, but we received separate errors that I may make another post about at a later time).