v0.6.4

• create linear reads BAM file
• create linear reads BigWigs for each region in the .regions file.

v0.6.3

• QOS not working for Taka... removed from cluster.json
• recall rule requires python/3.7 ... env module updated

v0.6.2

BSJ files are in BSJ subfolder... bug fix for v0.6.1

v0.6.1

• customBSJs recalled from STAR alignments
  • only for PE
  • removes erroneously called CircExplorer BSJs
• create sense and anti-sense BSJ BAMs and BW for each reference (host+viruses)
• find reads which contribute to CIRI BSJs but not on the STAR list of BSJ reads, see if they contribute to novel (not called by STAR) BSJs and append novel BSJs to customBSJ list

v0.6

cutadapt_min_length to cutadapt rule... setting it to 15 in config (f…

v0.5.5

• STAR2p output per gene counts and these per sample counts are aggregated into 3 count matrices:
  • stranded
  • unstranded
  • reverse stranded
• config.yaml now includes 3 resource paths:
  • original: hg38(masked) + rRNA + ERCC + legacy virus set from Mahesh
  • v2: original + HSV1 strain 17
  • v3: original + HSV1 KOS strain (with only 1 copy of repeats) --> this is now the new default

v0.5.4

• quant.txt annotation bug fix
• WORKDIR can now be a relative path
• bam2bw conversion fix for BSJ and spliced_reads. Issue closed!

v0.5.2

• Using picard to estimate duplicates using MarkDuplicates
• Generating a per-run multiqc HTML report
• Using eulerr R package to generate CIRI-CircExplorer circRNA Venn diagrams and include them in the mulitqc report
• Gather per job cluster metadata like queue time, run time, job state etc. Stats are compiled in HPC_summary file
• CLEAR pipeline quant.txt file is annotated for known circRNAs

v0.5.1

• venn diagram is now colored and scaled .. (using eulerr)

v.0.5.0

• run_clear is now set to True (as default)
• circ_quant replaces clear_quant in the CLEAR rule. In order words, we are reusing the STAR alignment file and the circExplorer2 output file for running CLEAR. No need to run HISAT2 and TopHat (fusion-search with Bowtie1). This is much quicker.