Same-description different sequence transcripts can now be collapsed by level of sequence identity
DESeq is now utilized even when there are no replicates in both conditions
Output fold change (2>1) column replaced with log2FoldChange
A version compatible with both DESeq versions
A version compatible only with DESeq versions >=1.5 (will be fixed in following versions)
- Updated SEQ-EM functionality, making it more memory efficient
- Removed fastx toolkit dependancy
- Removed bwa version < 0.58 support
- Improved separate mapped unmapped functionality
- Added ea-utils' fastq-mcf tool to allow quality trimming and adapter clipping for all types of input files.
- Minor code revisions for increased usability
- Multiple adapters clipping is now supported (using adapters.fa file)
- Changed RNA types annotations, RandA now supports cis-regulatory elements, antisense RNA, splicosomal RNAs and ribozymes.
- Removed Bioperl prerequisite.
- Improved error handling.