Added the following modification to NGSplot rule in all transcriptome (RNA-seq and MARS-seq) and chromatin (ChIP-seq and ATAC-seq) pipelines :
running time limitation of one hour
samples limitation to the first 10 samples
if NGSplot rule fails to run the pipeline will keep running
Temporarily (until we will upgrade the R version) removing MA plots generated with Glimma package from the report.
Corrected uncentered Pearson correlation to centered Pearson correlation in dendrogram and all heatmaps figures
Limiting Single-Cell pipeline usage to BBCU unit only.
Correct the Collaboration path to all class users
Made e-learning accessible without login.
Added more validation to the input fastq folder in all pipelines.
Added more validation to the report folder name and to the "run DESeq2 again" folder name
Fix bugs with ChIP-seq pipeline
Added scroll bar to large figures in the report.
Correct the number of threads in Single-Cell pipeline
Added Ribo-Seq pipeline (available to BBCU users only)
Remove the send button to the intermine site when the chosen genome is human (need to update the site api for human genome, the old site is no longer available for human genome).
Added UTAP version to all pipelines reports
Corrected phrasing in transcriptome reports
Converted UTAP to secure site
Add Plasmodium falciparum and Homo sapiens+Plasmodium falciparum genomes
Added a new pipeline - ChIP-Seq pipeline.
Added proposed changes in the ATAC-seq pipeline.
Added “advanced parameters” feature to enable customization of selected runtime parameters.
Added progress bar representation for each run
Added the columns “padj.after.FDR.correction” and “pass.after.FDR” to the Deseq_all_results.txt file where relevant.
Added the column “pass after FDR” to “Table 2: Links to functional enrichment analysis” in the report.html file where relevant.
Matched the PCA sample's colors to the ones in the dendrogarph in the report.html file.
Added the following STAR genomes: Chinese Hamster genome (chok1) and Danio rerio (Zebrafish) version 11 genome (danRer11).
Added bowtie genome - hg38 to the ChIP-Seq and ATAC-seq pipelines.
Changed project name field label to be more informative for the user.
Restricts single cell pipeline to internal users only (BBCU users).
Changed the UTAP emails according to Jaime’s and Marilyn’s requests.