stranded paired end data lead to unstranded bigWig files

[constadakis]

Hi all,

we use paired end fastq files from stranded libraries and get erroneous bigWig files from pigx-rnaseq.
the visualized tracks are not stranded.
the bam files though seem to be correct. using samtools and deeptools on them allows for the generation of correct looking bigWig files.

best,
Konsta

[borauyar]

@constadakis I updated the pipeline to use deepTools bamCoverage for creating bigwig files (will be available from version 0.0.16).