[rsem-announce] RSEM v1.2.7 has a minor update

[bli]

Hi all,

RSEM v1.2.7 has a minor update. One line is added to the 'WHAT_IS_NEW'
file to reflect a change made but forgotten to put in to 'WHAT_IS_NEW'.
The line added is "Renamed '--phred33-quals', '--phred64-quals', and
'--solexa-quals' in 'rsem-calculate-expression' to
'--bowtie-phred33-quals', '--bowtie-phred64-quals', and
'--bowtie-solex-quals' to avoid confusion".

Please *** note *** that the source code is not changed. What changed is
only the WHAT_IS_NEW file, thus you do not need to re-download the
package. Just be aware there is one more difference between RSEM v1.2.7
and RSEM v1.2.6.

The updated WHAT_IS_NEW looks like:
- 'rsem-find-DE' is replaced by 'rsem-run-ebseq' and 'rsem-control-fdr'
for a more friendly user experience
- Added support for differential expression testing on more than 2
conditions in RSEM's EBSeq wrappers 'rsem-run-ebseq' and
'rsem-control-fdr'
- Renamed '--phred33-quals', '--phred64-quals', and '--solexa-quals' in
'rsem-calculate-expression' to '--bowtie-phred33-quals',
'--bowtie-phred64-quals', and '--bowtie-solex-quals' to avoid confusion


You can find the source codes here
http://deweylab.biostat.wisc.edu/rsem/

Best,
Bo

[bli]

Hi all,

RSEM v1.2.8 is released now!

The updates include

- Provided a more detailed description for how to simulate RNA-Seq data
using 'rsem-simulate-reads'
- Provided more user-friendly error message if RSEM fails to extract
transcript sequences due to the failure of reading certain chromosome
sequences

You can find the latest version from

http://deweylab.biostat.wisc.edu/rsem/

Best,
Bo

[bli]

Hi all,

RSEM v1.2.9 is released now!

The updates include

- Fixed a compilation error problem in Mac OS
- Fixed a problem in makefile that affects 'make ebseq'
- Added 'model_file_description.txt', which describes the format and
meanings of file 'sample_name.stat/sample_name.model'
- Updated samtools to version 0.1.19

[bli]

Hi all,

RSEM v1.2.10 is released now!

The updates include

- Fixed a bug which will lead to out-of-memory error when RSEM computes
ngvector for EBSeq

[Bo Li]

Hi all,

RSEM v1.2.11 is released now!

The updates include

- Enabled RSEM to use Bowtie 2 aligner (indel, local and discordant
alignments are not supported yet)

- Changed option names '--bowtie-phred33-quals',
'--bowtie-phred64-quals' and '--bowtie-solexa-quals' back to
'--phred33-quals', '--phred64-quals' and '--solexa-quals'

[Bo Li]

Hi all,

RSEM v1.2.12 is released now!

The updates include

- Enabled allele-specific expression estimation
- Added '--calc-pme' option for 'rsem-calculate-expression' to calculate
posterior mean estimates only (no credibility intervals)
- Modified the shebang line of RSEM perl scripts to make them more
portable
- Added '--seed' option for 'rsem-simulate-reads' to enable users set
the seed of random number generator used by the simulation
- Modified the transcript extraction behavior of
'rsem-prepare-reference'. For transcripts that cannot be extracted,
instead of failing the whole script, warning information is produced.
Those transcripts are ignored

[Bo Li]

Hi all,

RSEM v1.2.13 is released now!

The updates include

- Allowed users to use the SAMtools in the PATH first and enabled RSEM
to find its executables via a symbolic link
- Changed the behavior of parsing GTF file. Now if a GTF line's feature
is not "exon" and it does not contain a "gene_id" or "transcript_id"
attribute, only a warning message will be produced (instead of failing
the RSEM)

[Bo Li]

Hi all,

RSEM v1.2.14 is released now!

The updates include

- Changed RSEM's behaviors for building Bowtie/Bowtie 2 indices. In
'rsem-prepare-reference', '--no-bowtie' and '--no-ntog' options are
removed. By default, RSEM does not build either Bowtie or Bowtie 2
indices. Instead, it generates two index Multi-FASTA files,
'reference_name.idx.fa' and 'reference_name.n2g.idx.fa'. Compared to the
former file, the latter one in addition converts all 'N's into 'G's.
These two files can be used to build aligner indices for customized
aligners. In addition, 'reference_name.transcripts.fa' does not have
poly(A) tails added. To enable RSEM build Bowtie/Bowtie 2 indices,
'--bowtie' or '--bowtie2' must be set explicitly. The most significant
benefit of this change is that now we can build Bowtie and Bowtie 2
indices simultaneously by turning both '--bowtie' and '--bowtie2' on.
Type 'rsem-prepare-reference --help' for more information
- If transcript coordinate files are visualized using IGV,
'reference_name.idx.fa' should be imported as a genome (instead of
'reference_name.transcripts.fa'). For more information, see the third
subsection of Visualization in 'README.md'
- Modified RSEM perl scripts so that RSEM directory will be added in the
beginning of the PATH variable. This also means RSEM will try to use its
own samtools first
- Added --seed option to set random number generator seeds in
'rsem-calculate-expression'
- Added posterior standard deviation of counts as output if either
'--calc-pme' or '--calc-ci' is set
- Updated boost to v1.55.0
- Renamed makefile as Makefile
- If '--output-genome-bam' is set, in the genome BAM file, each
alignment's 'MD' field will be adjusted to match the CIGAR string
- 'XS:A:value' field is required by Cufflinks for spliced alignments. If
'--output-genome-bam' is set, in the genome BAM file, first each
alignment's 'XS' filed will be deleted. Then if the alignment is an
spliced alignment, a 'XS:A:value' field will be added accordingly
- Added instructions for users who want to put all RSEM executables into
a bin directory (see Compilation & Installation section of 'README.md')

[Bo Li]

Hi all,

RSEM v1.2.15 is released now!

The updates include

- Allowed for a subset of reference sequences to be declared in an input
SAM/BAM file
- For any transcript not declared in the SAM/BAM file, its PME estimates
and credibility intervals are set to zero
- Added advanced options for customizing Gibbs sampler and credibility
interval calculation behaviors
- Splitted options in 'rsem-calculate-expression' into basic and
advanced options

[Bo Li]

Hi all,

RSEM v1.2.16 is released now!

The updates include

－ Corrected a typo in 'rsem-generate-data-matrix', this script extracts
'expected_count' column instead of 'TPM' column。

[Bo Li]

Hi all,

RSEM v1.2.17 is released now!

The updates include

－ Added error detection for cases such as a read's two mates having
different names or a read is both alignable and unalignable

[Bo Li]

Hi all,

RSEM v1.2.18 is released now!

The updates include

- Only generate warning message if two mates of a read pair have
different names
- Only parse attributes of a GTF record if its feature is "exon" to
avoid unnecessary warning messages

[Bo Li]

Hi all,

RSEM v1.2.19 is released now!

The updates include

- Modified 'rsem-prepare-reference' such that by default it does not add
any poly(A) tails. To add poly(A) tails, use '--polyA' option
- Added an annotation of the 'sample_name.stat/sample_name.cnt' file,
see 'cnt_file_description.txt'

[Bo Li]

Hi everyone,

RSEM v1.2.20 is released now!

The updates include

- Fixed a problem that can lead to assertion error if any paired-end
read's insert size > 32767 (by changing the type of insertL in
PairedEndHit.h from short to int)

[Bo Li]

Hi everyone,

RSEM v1.2.21 is released now!

The updates include

- Strip read names of extra words to avoid mismatches of paired-end read
names

[Bo Li]

Hi everyone,

We have good news to share with you.

First, RSEM website is officially moved to GitHub. The new url is
http://deweylab.github.io/RSEM/.

Second, we released RSEM v1.2.23. The updates include

- Moved version information from WHAT_IS_NEW to rsem_perl_utils.pm in
order to make sure the '--version' option always output the version
information

- Fixed a typo in 'rsem-calculate-expression' that can lead an error
when '--star' is set and '--star-path' is not set

- Fixed a bug that can occasionally crash the RSEM simulator

- Added user-friendly error messages that are triggered when RSEM
detects invalid bases in the input FASTA file during reference building


Best,
Bo

[Bo Li]

Hi everyone,

FYI, RSEM begins to support STAR aligner since version v1.2.22
(https://github.com/deweylab/RSEM/releases/tag/v1.2.22), which we forgot
to advertise here. The default STAR aligner setting is the same as the
one used by the ENCODE3 pipeline.

Best,
Bo

[Bo Li]

Hi everyone,

RSEM v1.2.24 is released!

New updates include:

- RSEM will extract gene_name/transcript_name from GTF file when
possible; if extracted, gene_name/transcript_name will append at the end
of gene_id/transcript_id with an underscore in between

- Modified 'rsem-plot-model' to indicate the modes of fragment length
and read length distributions

- Modified 'rsem-plot-model' to present alignment statistics better
using both barplot and pie chart

- Updated 'EBSeq' to version 1.2.0

- Added coefficient of quartile variation in addition to credibility
intervals when '--calc-ci' is turned on

- Added '--single-cell-prior' option to notify RSEM to use a sparse
prior (Dir(0.1)) for single cell data; this option only makes sense if

'--calc-pme' or '--calc-ci' is set

You can download the latest version by visiting RSEM website:
http://deweylab.github.io/RSEM/

Best,
Bo

[Bo Li]

Hi everyone,

RSEM v1.2.24 is released!

New updates include:

- RSEM will extract gene_name/transcript_name from GTF file when

possible; however, it only appends them to the 'sample_name.*.results'
files if '--append-names' option is specified; unlike v1.2.24, this
version is compatible with STAR aligner even when '--append-names' is

[Bo Li]

Hi everyone,

RSEM v1.2.26 is released!

New updates include:

- 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

[Bo Li]

Hi everyone,

RSEM v1.2.27 is released!

New updates include:

- 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

[Bo Li]

Hi everyone,

RSEM v1.2.28 is released!

New updates include:

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

Note: For users using RSEM v1.2.27, please be sure to upgrade to RSEM
v1.2.28 since v1.2.27 contains bugs affecting RSEM's functionality.

[Bo Li]

Hi everyone,

RSEM v1.2.29 is released!

New updates include:

- 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

[Bo Li]

Hi everyone,

RSEM v1.2.30 is released!

New updates include:

- 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

[Bo Li]

Hi everyone,

RSEM v1.2.31 is released!

New updates include:

- 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

[Bo Li]

Hi everyone,

RSEM v1.3.0 is released! This release now includes the
recently-published prior-enhanced RSEM (pRSEM) methodology. pRSEM
allows for the integration of a complementary data set, such as
polymerase II ChIP-seq data, with RNA-seq data to improve transcript
abundance estimates. For more information, please see the paper
describing pRSEM:

Peng Liu, Rajendran Sanalkumar, Emery H. Bresnick, Sunduz Keles, and
Colin N. Dewey. Integrative analysis with ChIP-seq advances the limits
of transcript quantification from RNA-seq. Genome Research 2016
26:1124-1133.
http://genome.cshlp.org/content/26/8/1124.abstract

and its associated website:
https://deweylab.github.io/pRSEM/

Other updates in this release include:

- 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

[Bo Li]

Hi everyone,

RSEM v1.3.1 is released!

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