RSEM v1.3.3

• Added HISAT2 option (--hisat2-hca) using Human Cell Atlas SMART-Seq2 pipeline parameters
• Fixed a bug in RSEM simulator

RSEM v1.3.2

• Prevent RSEM from crashing when there is 0 aligned reads.
• Output theta and model files even there is no aligned reads.

RSEM v1.3.1

• Added --gff3-genes-as-transcripts option for rsem-prepare-reference. This option will allow RSEM to treat genes as transcripts.

RSEM v1.3.0

• Added Prior-Enhanced RSEM (pRSEM) as a submodule
• Introduced --strandedness <none|forward|reverse> option, --strand-specific and --forward-prob are deprecated (but still supported)
• Revised documentation for rsem-plot-model, maked it clear that in alignment statistics, isoform-level (instead of genome-level) multi-mapping reads are shown
• Significantly improved the output information of rsem-sam-validator: if indels/clippings/skips are detected in alignments or alignments exceed transcript boundaries, rsem-sam-validator will report them instead of telling you the input is valid
• Updated the warning message to ask users to make sure that they align their reads agains a set of transcripts instead of genome when RSEM finds less sequences in the BAM file than RSEM's indices

RSEM v1.2.31

• Rewrote rsem-gff3-to-gtf to handle a more general set of GFF3 files
• Added safety checks to make sure poly(A) tails are not added to the reference when --star is set

RSEM v1.2.30

• Fixed a bug that can cause SAMtools sort to fail
• Improved the appearance of warning messages: for the same type of warning messages, only show the first 50 messages and then provide the total number of such warnings

RSEM v1.2.29

• Reformatted Makefile to be more professional, and make install is ready to use
• Enabled ./configure --without-curses for configuring SAMtools to avoid potential compilation problems due to curses library
• Fixed bugs for installing EBSeq
• Improved the readability of RSEM documentation

RSEM v1.2.28

• Fixed a bug in RSEM v1.2.27 that can lead to assertion errors for parsing GTF files
• Fixed a bug in Makefile

RSEM v1.2.27

• Upgraded SAMtools to v1.3; RSEM now supports input alignments in SAM/BAM/CRAM format
• '--sam/--bam' options of 'rsem-calculate-expression' are obsoleted; use '--alignments' instead; '--sam/--bam' can still be used for compatibility with previous versions
• Some 'rsem-calculate-expression' options are renamed for better interpretability
• Documents are updated to reflect the SAMtools upgrade
• Fixed a bug for parsing GTF files
• Fixed a bug for generating transcript wiggle plots

RSEM v1.2.26

• RSEM supports GFF3 annotation format now
• Added instructions to build RSEM references using RefSeq, Ensembl, or GENCODE annotations
• Added an option to extract only transcripts from certain resources given a GTF/GFF3 file
• Fixed a bug and improved the clarity of error messages for extracting transcripts from genome