After a review of our ATAC pipeline it was decided to add the following features to bripipetools:
[ ] TSSe score and plots automatically calculated
[ ] Generate fragment size distribution plots
[ ] split bam files
[ ] calculate FRiP scores and output a text file with list of file vs score - this should be possible using deeptools but requiring a dedicated python script from us
[ ] calculate PCA (with deeptools)
On the globus side:
[ ] We should investigate if there is a convincing reason to switch from STAR to bowtie2 aligner
After a review of our ATAC pipeline it was decided to add the following features to
bripipetools:bamfilesdeeptoolsbut requiring a dedicated python script from usdeeptools)On the globus side: