Extract regions of significantly different genes

Next we will extract read data of genes that were differentially expressed between the wild-type and knockout RNA-seq data.
By filtering our pre-existing BAM files to include only regions where there was differential gene expression, we can later visualize how the binding of our transcription factor Prep1 regulates these genes.
In Galaxy select, "NGS SAMTools" from the tool bar on the left. Then, select "Filter SAM or BAM".
Select the multiple datasets option since we'll be in putting both the wild-type can knock out RNA-seq data
Next select the BED file we created from our workflow to extract these regions from the aligned reads.
Then select "Execute".
Again, you can observe the runtime progress in your history.
These jobs usually take about five minutes to complete.