Releases · deweylab/RSEM

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

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

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

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

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

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

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

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 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

Releases: deweylab/RSEM