0.111.0

Major changes are:

Generic joint analysis support for isoform calling is now also supported for ont single cell analysis using the -iso_joint option. Isoquant has stricter requirements for the detection of novel isoforms than for known ones. This can cause novel isoforms to be missed in some samples. Joint analysis works by first analysing all samples separately, and than using the novel isoforms found in any of the samples as "known/reference" ones in a reanalysis (still per sample), causing them to be more likely found (and counted) even in these lower evidence samples. If you have many samples, the number of artefactual "novel" transcripts can become too large to use as a reference (performance wise). With the option -iso_joint_min only novel transcripts found in at least samples are used as a reference in stage2, reducing the number of artefacts used drastically.

The command sc_demultiplex was added for demultiplexing singlecell results into different samples, based on a demultiplexing file assigning each cell to sample. (Such a file can be generated based on genomic variants or feature barcode sequencing)

Some improvements in sc barcode detection were made:

• find_barcodes handles the presence of multiple adapter matches in a read better (mapquality filter, location)
• Support for v4 and 5 prime 10x barcodes has been added

Support for finding and annotating UMIs in bulk RNA-seq has been added, and can be used with the -addumis option. Analysis using isoquant will also take the UMIs into account when quantifying genes/isoforms.

An alternative cluster distribution method that limits the number of concurrently submitted jobs was added: When using -d slurm, all jobs will be submitted immediately (in a manner jobs will only be run when jobs they are dependent on are finished). This can (for large analyses) submit thousands of jobs, causing problemson clusters that limit the number of submitted jobs. You can now use the options -d -dsubmit slurm to run (distributed) on a slurm cluster, while limiting the number of concurrently submitted jobs to . The disadvantage of this method is that the submitting command has to keep running until the entire command/pipeline is finished (as it is managing the jobs partly by itself).

A custom set of regions for distribution can be added to a genomereference, and used by the option -distrreg g. This allows for optimization of parallel analysis by splitting up regions that take a longer time to process (due to e.g. size of gene richmess).

In several places support for cram has been added

• the longshot option for variant calling can now also produce a haplotyped cram
• tsv2sam and sam2tsv support cram
• cg_tsvdiff added the option -refseq needed for comparing some cram files

dirR improvements

• Added Rscript support to dirR
• make sure specific versions of packages are installed

Updates

• isoquant 3.6.3
• modkit 0.4.2
• clair3 1.0.10 (also tries to detect which model best to use)

Several new functions were added in cg select

• ljoin : combine elements of a list with a given separator
• percentsum : sum of field as percent versus total sum in given column
• gpercentsum : sum of field versus total sum in given group (row) as percent

Various other improvements

• Added ubam support in scywalker
• Added cg sc_analysis_basic: basic singlecell report even if some data is missing
• Added cg bam_index (atomic by making temp first, sets time to be same as bam file)
• Added convenience command cg rm (that properly deletes shadowdirs)
• cg tsv2fasta - added option -idfield and -sequencedfield, if not given, check for several fieldnames

Full Changelog: 0.110.0...0.111.0