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BIMSBbioinfo / pigx_rnaseq

Bulk RNA-seq Data Processing, Quality Control, and Downstream Analysis Pipeline
GNU General Public License v3.0
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stranded paired end data lead to unstranded bigWig files #69

Closed constadakis closed 3 years ago

constadakis commented 4 years ago

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 commented 3 years ago

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