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USeq full changelog

USeq full changelog

USeq 8.9.6 released Sep 28, 2015 (New Release)
Modified the per region spreadsheet to show the FracBPs>= xxx to be defined by the users minimum coverage setting.
Now gzipping pass and fail bed file outputs
USeq 8.9.5 released Aug 12, 2015 (New Release)
Bed2UCSCRefFlat
New app for converting a bed file to a multi exonic UCSC RefFlat file
Sam2USeq
USeq 8.9.3 released Jul 2, 2015 (New Release)
Bed2UCSCRefFlat
New app for converting a bed file to a multi exonic UCSC RefFlat file
Sam2USeq
USeq 8.8.8 released Jan 7, 2015 (New Release)
Major bug! The filter for selecting vcf variants for those in common regions was inadvertently disabled. Ugg! To findout if your prior analysis as affected, look at the # of pre and post filtered variants these should differ, if not discard! Drat!
USeq 8.8.7 released Dec 16, 2014 (New Release)
Renamed to CollectBamStats
Added a bunch of functionality to collect both read coverage data and alignment stats from the MergePairedAlignments and Sam2USeq apps
MergePairedAlignments
USeq 8.8.5 released Nov 10, 2014 (New Release)
Added option to filter by region
Cleaned up chunking issues when no chunking is indicated
USeq 8.8.4 released Aug 11, 2014 (New Release)
MergeSams
Created a new app to merge sam and bam files. Creates a stripped header from the files if one isn't provided. This won't play nicely with downstream GATK or Picard apps. Have yet to find at good app for doing this, SamTools and Picard's are riddled with error/ validation headaches.
DefinedRegionDifferentialSeq
Added catch for alignments that are run off the end of the last reported base in a chromosome
USeq 8.8.2 released Aug 11, 2014 (New Release)
ReferenceMutator
New app that takes a directory of fasta chromosome sequence files and converts the reference allele to the alternate provided by a snp mapping table
SamComparator
New app that compares two sam/bam files and splits those into matching and non matching based on coordinates. Good for allele specific expression analysis
DefinedRegionDifferentialSeq
Added option to collect counts from the 5' and 3' ends of genes
DifferentialReadCoverageComparator
Takes the count table generated by DRDS with the -z option and looks for changes in 5'/3' read coverage between different conditions to identify short truncated transcripts
RandomMutationGenerator
Creates snvs and indels for the BAMSurgeon application
USeq 8.8.1 released Jul 23, 2014 (New Release)
Updated DESeq to DESeq2, major changes, different dispersion fit, different log2Rto calculation, automatic independence filtering. All results in more diff expressed genes compared to the older depreciated methods. Old diff genes are pretty much a subset of new diff genes.
USeq 8.8.0 released May 12, 2014 (New Release)
Updated DESeq to DESeq2, major changes, different dispersion fit, different log2Rto calculation, automatic independence filtering. All results in more diff expressed genes compared to the older depreciated methods. Old diff genes are pretty much a subset of new diff genes.

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Full USeq 8.9.6 details

Download USeq 8.9.6



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