bam2wig.py -s chrom.sizes -i sample.bam -o out [options]
bam2wig.py converts all types of RNA-seq data from BAM format into wiggle format. If UCSC
wigToBigWig tool was found, output wiggle file will be converted into bigwig format automatically. BAM file must be
indexed properly using samtools. Below example shows how to sort and index BAM file using samTools
indexedproperly using samtools. .bam and .bai files should be placed in the same directory.
--strand='1++,1--,2+-,2-+'means that this is a pair-end, strand-specific RNA-seq data, and the strand rule is:
If you are not sure about the strand rule, run
infer_experiment.py. default=none (Not a strand specific RNA-seq data).
STAR, can directly generate wig files.