Support for SBARRO experiments

[jamesnemesh]

Support for SBARRO experiments 

• TagReadWithRabiesBarcodes - Tags an unaligned BAM with rabies virus barcode sequences and associated metrics. Barcode sequences are extracted using invariant sequences which flank the barcode regions.
• FilterValidRabiesBarcodes - Filters rabies virus tags into pass/fail BAMs based on metrics associated with the extracted viral barcodes.
• BipartiteRabiesVirusCollapse - Collapse rabies virus sequences in which half the barcode matches within some edit distance, within a cell.
   

Other updates

• TrimStartingSequence update:  New algorithm with mismatch rate and sequence not require to be anchored to start of read.  Note that different sequence is recommended for 10X and Drop-seq.  Old, buggy behavior can be enabled with LEGACY=true.
• PolyATrimmer now optionally stores length of polyA and trimmed adapter
• ConvertTagToReadGroup improved error messages when read group missing from input data
• FilterBamByGeneFunction - new program to filter reads to specified gene functions, in the same way DigtialGeneExpression and related programs internally filter data.
• CensusSeq and related software can now take as input a list of BAMs.
• Csi analysis now generates a contamination confidence interval.
• Improvements to make GTF parsing more robust

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This discussion was created from the release Support for SBARRO experiments.

[tlz4320]

Hello! I'm reading SBARRO paper these days. But I didn't find the code to calculate whether the VBC is unique in this code repo. Could you please provide how to find the unique VBC. This is a very important part algorithm in SBARRO paper.