USeq Source Code

DefinedRegionDifferentialSeq
* Added a System.setProperty("java.awt.headless", "true") to allow running app in non x11 mode.

VCFSample
* Changed how it recognizes a no call to anything that starts with ./. so these are skipped

FilterIntersectingRegions
* Added option to split gtf/ gff files

*Added support for BWA mem. This broke some of the USeq apps that expect a single alignment per pair and didn't check the primary flag.
*Remove hard-coded paths to software and added them to the config file. I don't like a user-specified config file... I need to come up with a better solution
*Changed the names of the output VCF files, 'filtered' and 'passing' was too cryptic. Files are now 'filterFieldSetAll' and 'filterFieldSetPassing', much clearer?
*Merged 'primary' and 'padded' target bed file and added AgilentV5UTR to list.

GATK and Annovar format InDels differently. InDels were labeled 'substitutions', now they are properly labeled insertions and deletions.

TomatoFarmer Update

1. Fixed soft-linking of 101bp paired-end RNA-Seq data
2. Added updated alignments params for 101bp paired-end RNA-Seq data
3. Updated sequencing application codes to include new applications and removed outdated ones
4. Updated miRNA alignment params
5. Removed code to make the QC, processedAlignments, and coverageTracks dirs in GNomEx, as it appears that most users delete them and make their own
6. Changed dir path of tomato/job/ to /tomato/dev/job/ to work with Tomato3
7. Changed path of autoalignerData to /tomato/dev/job/autoaligner/autoalignerData/
8. Changed path of apps to /tomato/dev/job/autoaligner/apps/
9. Changed the number of lines in each split bisulfite fastq file to cut down on file #

Latest comments

Added catch to rename broken useq archives so these are skipped in subsequent autoconversion

Added catch for fetching last bases from an array of regions

Updated apps to work with kingspeak cluster and use rsync for all transfers

Added catch for fetching last bases from an array of regions