RSEM v1.1.12 is released!
Bo Li
RSEM v1.1.12 is online now. Add a script for generating
transcript-to-gene-map file from Trinity output. Claim the minimum seed
length explicitly. Allow empty sequences in the reference fasta file.
You can find the source code here
http://deweylab.biostat.wisc.edu/rsem/
Best,
Bo
b...@cs.wisc.edu
I just realize that the perl script I provide has some problems. It is
already fixed now and please download the rsem v1.1.12 again from our
website. Sorry for the inconvenient. Please also note that the script does
not require any third party package.
Best,
Bo
Bo Li
RSEM v1.1.13 is online now. Speed up EM algorithm by only updating model
parameters for first 10 iterations. Skip reads with its (or at least one
of its mates', for paired-end reads) length < 25bp.
Bo Li
RSEM v1.1.14 is online now.
In this version of RSEM, several things are updated:
- Added --chunkmbs option to rsem-calculate-expression (patch
contributed by earonesty)
- Added --sampling-for-bam option to rsem-calculate-expression, in the
bam file, instead of providing expected weights, for each read RSEM
samples one alignment based on the expected weights
- RSEM can generate BAM and Wiggle files in both genomic-coordinate and
transcript-coordinate
- Added rsem-plot-transcript-wiggles. This script can generate
transcript-coordinate wiggle plots in pdf format. One unique feature is,
a stacked plot can be generated, with unique read contribution shown as
black and multi-read contribution shown as red
- Added convert_sam_for_rsem script for users do not use bowtie aligner
- Modified RSEM's GTF file parser. Now RSEM does not require
"transcript_id" and "gene_id" be the first two attributes shown
- Improved descriptions for thread related errors.
Bo Li
RSEM v1.1.14 is online now.
Bugs causing compilation failure are fixed. Modified samtools' Makefile
to compile it successfully in cygwin.
You can find the source codes here
http://deweylab.biostat.wisc.edu/rsem/
Best,
Bo
Bo Li
RSEM v1.1.15 is online now.
Bugs causing compilation failure are fixed. Modified samtools' Makefile
to compile it successfully in cygwin.
You can find the source codes here
http://deweylab.biostat.wisc.edu/rsem/
Best,
Bo
Bo Li
RSEM v1.1.15 is online now.
- Fixed several bugs causing compilation error
- Modified samtools' Makefile for cygwin. For cygwin users, please
uncomment the 4th and 8th lines in sam/Makefile before compiling RSEM
You can find the source codes here
http://deweylab.biostat.wisc.edu/rsem/
Please re-download if you have downloaded rsem-1.1.15.tar.gz before this
email. The package uploaded was not correct but now it is fixed.
Best,
Bo
Bo Li
RSEM v1.1.17 is online now.
- Fixed a bug related to parallezation of credibility intervals calculation
- Added --no-bam-output option to rsem-calculate-expression
- The order of @SQ tags in SAM/BAM files can be arbitrary now
You can find the source codes here
http://deweylab.biostat.wisc.edu/rsem/
Best,
Bo
b...@cs.wisc.edu
we have just released a Galaxy wrapper for RSEM in the Galaxy tool shed:
http://toolshed.g2.bx.psu.edu/
(it's under the "sequence analysis" category)
Best,
Bo
Bo Li
RSEM v1.1.18 is online now.
- Added some user-friendly error messages
- Added program 'rsem-sam-validator', users can use this program to
check if RSEM can process their SAM/BAM files
- Modified 'convert-sam-for-rsem' so that this program will convert
users' SAM/BAM files into acceptable BAM files for RSEM
You can find the source codes here
http://deweylab.biostat.wisc.edu/rsem/
Best,
Bo
Bo Li
There is a bug in GCC (version 4.5.3 or higher) which will make RSEM
fail to compile. For people who use GCC version 4.5.3 or higher, please
download the modified version using the below link:
https://github.com/bli25wisc/RSEM/zipball/v1.1.18_modified
Best,
Bo