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 sorted
and indexed
properly using samtools. Below example shows how to sort and index BAM file using samTools
sorted
and indexed
properly using samtools. .bam and .bai files should be placed in the same directory.fetchChromSize
and twoBitInfo
.--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.PINTS visualizer
.