rsem.git
5 years agoinstall the rsem_perl_utils.pm to /usr/bin even though this is wrong debian
Don Armstrong [Thu, 20 Nov 2014 21:46:05 +0000 (13:46 -0800)]
install the rsem_perl_utils.pm to /usr/bin even though this is wrong

5 years agoadd debian packaging
Don Armstrong [Mon, 29 Sep 2014 18:22:36 +0000 (11:22 -0700)]
add debian packaging

5 years agoMerge tag 'upstream/1.2.17' into debian
Don Armstrong [Mon, 29 Sep 2014 18:06:18 +0000 (11:06 -0700)]
Merge tag 'upstream/1.2.17' into debian

Upstream version 1.2.17

5 years agoImported Upstream version 1.2.17 upstream
Don Armstrong [Mon, 29 Sep 2014 18:06:14 +0000 (11:06 -0700)]
Imported Upstream version 1.2.17

5 years agoImported Upstream version 1.2.17
Don Armstrong [Mon, 29 Sep 2014 18:05:47 +0000 (11:05 -0700)]
Imported Upstream version 1.2.17

5 years agoImported Upstream version 1.2.17
Don Armstrong [Mon, 29 Sep 2014 18:05:28 +0000 (11:05 -0700)]
Imported Upstream version 1.2.17

5 years agoImported Upstream version 1.2.17
Don Armstrong [Mon, 29 Sep 2014 18:04:17 +0000 (11:04 -0700)]
Imported Upstream version 1.2.17

5 years agoAdded error detection for cases such as a read's two mates having different names... master
Bo Li [Wed, 3 Sep 2014 21:43:53 +0000 (16:43 -0500)]
Added error detection for cases such as a read's two mates having different names or a read is both alignable and unalignable

5 years agoModified WHAT_IS_NEW
Bo Li [Mon, 18 Aug 2014 20:43:43 +0000 (15:43 -0500)]
Modified WHAT_IS_NEW

5 years agoCorrected a typo in rsem-generate-data-matrix
Bo Li [Mon, 11 Aug 2014 19:40:26 +0000 (14:40 -0500)]
Corrected a typo in rsem-generate-data-matrix

5 years agoAdded .gitignore file back
Bo Li [Thu, 19 Jun 2014 22:23:39 +0000 (17:23 -0500)]
Added .gitignore file back

5 years agoDeleted a ';' at the end of RSEM v1.2.15 updates
Bo Li [Mon, 16 Jun 2014 08:32:47 +0000 (03:32 -0500)]
Deleted a ';' at the end of RSEM v1.2.15 updates

5 years agoUpdated WHAT_IS_NEW
Bo Li [Mon, 16 Jun 2014 08:25:37 +0000 (03:25 -0500)]
Updated WHAT_IS_NEW

5 years agoAllowed for a subset of reference sequences to be declared in an input SAM/BAM file...
Bo Li [Mon, 16 Jun 2014 08:23:12 +0000 (03:23 -0500)]
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.

5 years agoAdded advanced options for customizing Gibbs sampler and credibility interval calcula...
Bo Li [Sun, 15 Jun 2014 21:21:36 +0000 (16:21 -0500)]
Added advanced options for customizing Gibbs sampler and credibility interval calculation behaviors; Splitted options in 'rsem-calculate-expression' into basic and advanced options; stopped tracking of .gitignore file

5 years agoAdded .gitignore to ignore built files
Colin Dewey [Fri, 13 Jun 2014 16:17:01 +0000 (11:17 -0500)]
Added .gitignore to ignore built files

5 years agoRemoved Mac ._* files from repo
Colin Dewey [Fri, 13 Jun 2014 16:15:18 +0000 (11:15 -0500)]
Removed Mac ._* files from repo

5 years agoUpdated README.md and WHAT_IS_NEW
Bo Li [Mon, 9 Jun 2014 04:48:03 +0000 (23:48 -0500)]
Updated README.md and WHAT_IS_NEW

5 years agoFor genome BAM, modified MD tag accordingly
Bo Li [Sun, 8 Jun 2014 12:18:22 +0000 (07:18 -0500)]
For genome BAM, modified MD tag accordingly

5 years agoRenamed makefile as Makefile
Bo Li [Sun, 8 Jun 2014 00:45:27 +0000 (19:45 -0500)]
Renamed makefile as Makefile

5 years agoModified the use of uniform_01
Bo Li [Fri, 6 Jun 2014 10:41:46 +0000 (05:41 -0500)]
Modified the use of uniform_01

5 years agoUpdated boost to v1.55.0
Bo Li [Fri, 6 Jun 2014 09:15:18 +0000 (02:15 -0700)]
Updated boost to v1.55.0

5 years agoAdded posterior standard deviation of counts as output if either '--calc-pme' or...
Bo Li [Fri, 6 Jun 2014 08:50:21 +0000 (03:50 -0500)]
Added posterior standard deviation of counts as output if either '--calc-pme' or '--calc-ci' is set

5 years agoAdded --seed option to set random number generator seeds in 'rsem-calculate-expression'
Bo Li [Fri, 6 Jun 2014 03:53:28 +0000 (22:53 -0500)]
Added --seed option to set random number generator seeds in 'rsem-calculate-expression'

5 years agoModified RSEM perl scripts so that RSEM directory will be added in the beginning...
Bo Li [Thu, 5 Jun 2014 19:46:52 +0000 (14:46 -0500)]
Modified RSEM perl scripts so that RSEM directory will be added in the beginning of PATH variable

6 years agoRemoved '--no-bowtie' and '--no-ntog' options in 'rsem-prepare-reference' and put...
Bo Li [Thu, 5 Jun 2014 08:58:43 +0000 (03:58 -0500)]
Removed '--no-bowtie' and '--no-ntog' options in 'rsem-prepare-reference' and put only raw extracted sequences in 'reference_name.transcripts.fa'

6 years agoGenerated two index multi-Fasta files instead, one without 'N' converted to 'G' and...
Bo Li [Thu, 5 Jun 2014 07:20:01 +0000 (02:20 -0500)]
Generated two index multi-Fasta files instead, one without 'N' converted to 'G' and one with 'N' converted to 'G'.

6 years agoWHAT_IS_NEW is updated
Bo Li [Tue, 27 May 2014 01:28:00 +0000 (20:28 -0500)]
WHAT_IS_NEW is updated

6 years agoChanged the behavior of parsing GTF file. Now if a GTF line's feature is not exon...
Bo Li [Tue, 27 May 2014 01:06:54 +0000 (20:06 -0500)]
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)

6 years agoUse PATH env to instead the variable
Bo Li [Thu, 3 Apr 2014 17:30:24 +0000 (12:30 -0500)]
Use PATH env to instead the  variable

6 years agoModified the acknowledgement section of README.md
Bo Li [Thu, 27 Mar 2014 23:33:05 +0000 (18:33 -0500)]
Modified the acknowledgement section of README.md

6 years ago Modified the transcript extraction behavior of 'rsem-prepare-reference'. For transcr...
Bo Li [Thu, 27 Mar 2014 23:07:42 +0000 (18:07 -0500)]
 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

6 years agoAdded '--seed' option for 'rsem-simulate-reads'
Bo Li [Sat, 22 Mar 2014 04:53:57 +0000 (23:53 -0500)]
Added '--seed' option for 'rsem-simulate-reads'

6 years agoModified the shebang line for perl scripts
Bo Li [Fri, 21 Mar 2014 20:05:03 +0000 (15:05 -0500)]
Modified the shebang line for perl scripts

6 years agoAdded support for allele-specific expression estimation
Bo Li [Fri, 21 Mar 2014 16:27:31 +0000 (11:27 -0500)]
Added support for allele-specific expression estimation

6 years agoFixed a typo in rsem-calculate-expression's document; Added multi-thread and memory...
Bo Li [Sun, 9 Mar 2014 20:40:25 +0000 (15:40 -0500)]
Fixed a typo in rsem-calculate-expression's document; Added multi-thread and memory options to samtools sort thanks to Dr. Samuel Arvidsson

6 years agoAdded Bowtie 2 support
Bo Li [Fri, 14 Feb 2014 15:26:47 +0000 (09:26 -0600)]
Added Bowtie 2 support

6 years agoFixed a bug which will lead to out-of-memory error when RSEM computes ngvector for...
Bo Li [Sat, 1 Feb 2014 00:03:52 +0000 (18:03 -0600)]
Fixed a bug which will lead to out-of-memory error when RSEM computes ngvector for EBSeq

6 years agoRemoved unnecessary spaces in POD doc of rsem-calculate-expression'
Bo Li [Sat, 11 Jan 2014 20:17:32 +0000 (14:17 -0600)]
Removed unnecessary spaces in POD doc of rsem-calculate-expression'

6 years agoAdded update samtools to WHAT_IS_NEW
Bo Li [Thu, 9 Jan 2014 06:32:54 +0000 (00:32 -0600)]
Added update samtools to WHAT_IS_NEW

6 years agoModified WHAT_IS_NEW for RSEM v1.2.9
Bo Li [Thu, 9 Jan 2014 05:55:49 +0000 (23:55 -0600)]
Modified WHAT_IS_NEW for RSEM v1.2.9

6 years agoFixed a problem that will lead compilation errors for Mac OS
Bo Li [Thu, 9 Jan 2014 00:56:45 +0000 (18:56 -0600)]
Fixed a problem that will lead compilation errors for Mac OS

6 years agoREADME.md is updated
Bo Li [Thu, 9 Jan 2014 00:45:35 +0000 (18:45 -0600)]
README.md is updated

6 years agoUpdated samtools to 0.1.19
Bo Li [Thu, 9 Jan 2014 00:26:18 +0000 (18:26 -0600)]
Updated samtools to 0.1.19

6 years agoAdded a file describing the format of sample_name.stat/sample_name.model
Bo Li [Mon, 2 Dec 2013 07:10:41 +0000 (01:10 -0600)]
Added a file describing the format of sample_name.stat/sample_name.model

6 years agoProvided a more detailed description for how to simulate RNA-Seq data using 'rsem...
Bo Li [Fri, 22 Nov 2013 12:06:00 +0000 (06:06 -0600)]
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

6 years agoAdded a line in WHAT_IS_NEW for renaming of quality score related options in 'rsem...
Bo Li [Wed, 25 Sep 2013 18:10:40 +0000 (13:10 -0500)]
Added a line in WHAT_IS_NEW for renaming of quality score related options in 'rsem-calculate-expression'

6 years agoFixed a displaying problem for rsem-run-ebseq's Pod document
Bo Li [Sat, 7 Sep 2013 10:52:33 +0000 (05:52 -0500)]
Fixed a displaying problem for rsem-run-ebseq's Pod document

6 years agoFixed loading library problem for EBSeq/install
Bo Li [Sat, 7 Sep 2013 10:38:50 +0000 (05:38 -0500)]
Fixed loading library problem for EBSeq/install

6 years agoFixed a bug for adding EBSeq's local library path
Bo Li [Sat, 7 Sep 2013 10:19:35 +0000 (05:19 -0500)]
Fixed a bug for adding EBSeq's local library path

6 years agoChanged WHAT_IS_NEW
Bo Li [Sat, 7 Sep 2013 09:54:33 +0000 (04:54 -0500)]
Changed WHAT_IS_NEW

6 years ago'rsem-run-ebseq': Added 'output_file.condmeans' for tests with more than 2 conditions
Bo Li [Sat, 7 Sep 2013 04:00:12 +0000 (23:00 -0500)]
'rsem-run-ebseq': Added 'output_file.condmeans' for tests with more than 2 conditions

6 years agoAdded support for DE analysis on multiple conditions via running EBSeq
Bo Li [Mon, 2 Sep 2013 08:25:23 +0000 (03:25 -0500)]
Added support for DE analysis on multiple conditions via running EBSeq

6 years agoRenamed --phred33-quals, --phred64-quals, and --solexa-quals to --bowtie-phred33...
Bo Li [Wed, 28 Aug 2013 22:11:30 +0000 (17:11 -0500)]
Renamed --phred33-quals, --phred64-quals, and --solexa-quals to --bowtie-phred33-quals, --bowtie-phred64-quals, and --bowtie-solex-quals to avoid confusion

6 years agoFixed a minor bug which only affects paired-end reads for reporting how many alignmen...
Bo Li [Wed, 21 Aug 2013 18:07:52 +0000 (13:07 -0500)]
Fixed a minor bug which only affects paired-end reads for reporting how many alignments are processed when RSEM generates BAM outputs

6 years agoInstall the latest version of EBSeq from Bioconductor and if fails, try to install...
Bo Li [Wed, 31 Jul 2013 07:19:15 +0000 (02:19 -0500)]
Install the latest version of EBSeq from Bioconductor and if fails, try to install EBSeq v1.1.5 locally. Fixed a bug in 'rsem-gen-transcript-plots', which makes 'rsem-plot-transcript-wiggles' fail

6 years agoFixed a bug in rsem-find-DE, which will crash the script if only one DE gene/isoform...
Bo Li [Thu, 4 Jul 2013 07:11:18 +0000 (02:11 -0500)]
Fixed a bug in rsem-find-DE, which will crash the script if only one DE gene/isoform is found

6 years agoUpdated EBSeq from v1.1.5 to v1.1.6 and fixed a bug in 'rsem-generate-data-matrix...
Bo Li [Wed, 26 Jun 2013 22:28:09 +0000 (17:28 -0500)]
Updated EBSeq from v1.1.5 to v1.1.6 and fixed a bug in 'rsem-generate-data-matrix', which can cause 'rsem-find-DE' to crash

7 years agoModifed README.md and WHAT_IS_NEW
Bo Li [Mon, 15 Apr 2013 16:48:12 +0000 (11:48 -0500)]
Modifed README.md and WHAT_IS_NEW

7 years agoModified wiggle.cpp & wiggle.h for more accurate floating point number arithmetics...
Bo Li [Mon, 15 Apr 2013 16:26:02 +0000 (11:26 -0500)]
Modified wiggle.cpp & wiggle.h for more accurate floating point number arithmetics. Modified rsem-gen-transcript-plots to output warning messages instead of exit the script when positions where multiread track has less coverage than uniq track are detected. Thanks Han Lin for pointing out the problem and suggesting possible fixes

7 years agoModified my_assert.h to postpone error message string generation
Bo Li [Mon, 15 Apr 2013 05:56:55 +0000 (00:56 -0500)]
Modified my_assert.h to postpone error message string generation

7 years agoRemoved a too stringent sanity check in rsem-gen-transcript-plots
Bo Li [Fri, 5 Apr 2013 18:16:29 +0000 (13:16 -0500)]
Removed a too stringent sanity check in rsem-gen-transcript-plots

7 years agoremove .gitignore from the staging area
Bo Li [Wed, 27 Mar 2013 00:54:53 +0000 (19:54 -0500)]
remove .gitignore from the staging area

7 years agoAdded some user-friendly error messages for BamConverter.h
Bo Li [Fri, 22 Mar 2013 01:01:53 +0000 (20:01 -0500)]
Added some user-friendly error messages for BamConverter.h

7 years agoModified rsem-tbam2gbam so that the original alignment quality MAPQ will be preserved...
Bo Li [Fri, 22 Mar 2013 00:43:06 +0000 (19:43 -0500)]
Modified rsem-tbam2gbam so that the original alignment quality MAPQ will be preserved if the input bam is not from RSEM

7 years agoFixed a bug that will lead perl scripts fail to find the perl module they use
Bo Li [Sun, 27 Jan 2013 15:19:02 +0000 (09:19 -0600)]
Fixed a bug that will lead perl scripts fail to find the perl module they use

7 years agoAdded user-friendly error messages if users forget to compile the source codes
Bo Li [Thu, 24 Jan 2013 16:22:52 +0000 (10:22 -0600)]
Added user-friendly error messages if users forget to compile the source codes

7 years agoFixed a bug in 'EBSeq/rsem-for-ebseq-generate-ngvector-from-clustering-info' which...
Bo Li [Tue, 8 Jan 2013 16:11:50 +0000 (10:11 -0600)]
Fixed a bug in 'EBSeq/rsem-for-ebseq-generate-ngvector-from-clustering-info' which may crash the script

7 years agoModified rsem-find-DE
Bo Li [Mon, 7 Jan 2013 13:14:51 +0000 (07:14 -0600)]
Modified rsem-find-DE

7 years agoUpdated EBSeq to v1.1.5
Bo Li [Mon, 7 Jan 2013 13:11:20 +0000 (07:11 -0600)]
Updated EBSeq to v1.1.5

7 years ago- Added poly(A) tails to 'reference_name.transcripts.fa' so that the RSEM generated...
Bo Li [Fri, 30 Nov 2012 03:43:49 +0000 (21:43 -0600)]
- Added poly(A) tails to 'reference_name.transcripts.fa' so that the RSEM generated transcript unsorted BAM file can be fed into RSEM as an input file. However, users need to rebuild their references if they want to visualize the transcript level wiggle files and BAM files using IGV
- Modified 'rsem-tbam2gbam' to convert users' alignments from transcript BAM files into genome BAM files, provided users use 'reference_name.idx.fa' to build indices for their aligners
- Updated EBSeq from v1.1.3 to v1.1.4
- Corrected several typos in warning messages

7 years agoUpdated EBSeq to v1.1.4
Bo Li [Sun, 21 Oct 2012 19:41:38 +0000 (14:41 -0500)]
Updated EBSeq to v1.1.4

7 years agoAdded --version option for rsem-calculate-expression
Bo Li [Thu, 18 Oct 2012 15:32:37 +0000 (10:32 -0500)]
Added --version option for rsem-calculate-expression

7 years agouse if/elsif to replace switch in rsem-calculate-expression
Bo Li [Wed, 10 Oct 2012 21:46:37 +0000 (16:46 -0500)]
use if/elsif to replace switch in rsem-calculate-expression

7 years agoFixed a bug to make RSEM generated BAM file valid input for RSEM
Bo Li [Mon, 24 Sep 2012 07:58:35 +0000 (02:58 -0500)]
Fixed a bug to make RSEM generated BAM file valid input for RSEM

7 years agoIf a gene is not expressed, its length/effective length is defined as the unweighted...
Bo Li [Sat, 15 Sep 2012 20:27:44 +0000 (15:27 -0500)]
If a gene is not expressed, its length/effective length is defined as the unweighted mean of its isoforms'

7 years agoREADME.md is changed
Bo Li [Tue, 11 Sep 2012 10:10:36 +0000 (05:10 -0500)]
README.md is changed

7 years agoAdded a script, 'rsem-find-DE', to run EBSeq automatically
Bo Li [Tue, 11 Sep 2012 09:07:43 +0000 (04:07 -0500)]
Added a script, 'rsem-find-DE', to run EBSeq automatically

7 years agochanged output format to contain FPKM etc. ; fixed a bug for paired-end reads
Bo Li [Mon, 10 Sep 2012 21:22:52 +0000 (16:22 -0500)]
changed output format to contain FPKM etc. ; fixed a bug for paired-end reads

7 years agoAdded a user-friendly error message for rsem-sam-validator
Bo Li [Fri, 27 Jul 2012 16:46:25 +0000 (11:46 -0500)]
Added a user-friendly error message for rsem-sam-validator

7 years agoFixed a bug for calling pthread_join
Bo Li [Mon, 23 Jul 2012 00:01:16 +0000 (19:01 -0500)]
Fixed a bug for calling pthread_join

7 years agoFixed a bug in perl scripts for printing error messages
Bo Li [Sun, 22 Jul 2012 02:11:07 +0000 (21:11 -0500)]
Fixed a bug in perl scripts for printing error messages

7 years agoFix a bug on convert-sam-for-rsem for the case that a paired-end read can align to...
Bo Li [Sun, 15 Jul 2012 20:46:46 +0000 (15:46 -0500)]
Fix a bug on convert-sam-for-rsem for the case that a paired-end read can align to the same position with different directions

7 years agorsem v1.1.21
Bo Li [Mon, 2 Jul 2012 17:18:03 +0000 (12:18 -0500)]
rsem v1.1.21

7 years agoTested the codes
Bo Li [Wed, 6 Jun 2012 02:02:46 +0000 (21:02 -0500)]
Tested the codes

7 years agoMade the BAM output of RSEM have all information contained in the input alignments...
Bo Li [Tue, 5 Jun 2012 21:25:13 +0000 (16:25 -0500)]
Made the BAM output of RSEM have all information contained in the input alignments file

8 years agoIncluded EBSeq for downstream differential expression analysis
Bo Li [Thu, 26 Apr 2012 13:50:22 +0000 (08:50 -0500)]
Included EBSeq for downstream differential expression analysis

8 years agoAdded some instructions on how to visualize transcript coordinate BAM/WIG files using IGV
Bo Li [Sun, 15 Apr 2012 13:27:02 +0000 (08:27 -0500)]
Added some instructions on how to visualize transcript coordinate BAM/WIG files using IGV

8 years agoFixed a bug related to intermediate output displaying in wiggle.cpp
Bo Li [Sat, 14 Apr 2012 03:22:03 +0000 (22:22 -0500)]
Fixed a bug related to intermediate output displaying in wiggle.cpp

8 years agoFixed a bug related to intermediate output displaying in EM.cpp
Bo Li [Fri, 13 Apr 2012 21:30:33 +0000 (16:30 -0500)]
Fixed a bug related to intermediate output displaying in EM.cpp

8 years agoAllowed > 2^31 hits
Bo Li [Wed, 21 Mar 2012 15:44:21 +0000 (10:44 -0500)]
Allowed > 2^31 hits

8 years agoModified makefile to work for gcc version 4.5.3 or higher
Bo Li [Sun, 11 Mar 2012 10:47:20 +0000 (05:47 -0500)]
Modified makefile to work for gcc version 4.5.3 or higher

8 years agoModified 'convert-sam-for-rsem' so that this program will convert users' SAM/BAM...
Bo Li [Sun, 11 Mar 2012 10:22:22 +0000 (05:22 -0500)]
Modified 'convert-sam-for-rsem' so that this program will convert users' SAM/BAM files into acceptable BAM files for RSEM

8 years agoAdd a validator for input SAM/BAM file
Bo Li [Sun, 11 Mar 2012 04:35:10 +0000 (22:35 -0600)]
Add a validator for input SAM/BAM file

8 years agoImproved warning messages in rsem-gen-transcript-plots
Bo Li [Fri, 9 Mar 2012 13:30:28 +0000 (07:30 -0600)]
Improved warning messages in rsem-gen-transcript-plots

8 years agoAdd warning messages for detected invalid alignments
Bo Li [Fri, 9 Mar 2012 04:36:05 +0000 (22:36 -0600)]
Add warning messages for detected invalid alignments

8 years agoAdded .gitignore to ignore build products
Colin Dewey [Mon, 27 Feb 2012 17:00:59 +0000 (11:00 -0600)]
Added .gitignore to ignore build products

8 years agoModified build rules for sam/libbam.a to enable parallel build
Colin Dewey [Mon, 27 Feb 2012 16:56:16 +0000 (10:56 -0600)]
Modified build rules for sam/libbam.a to enable parallel build

Thanks to Tomoaki Nishiyama for the suggestion.

8 years ago[Change] Do not add --phred33-qual option if --no-qualities is enabled
Bo Li [Sun, 19 Feb 2012 21:58:25 +0000 (15:58 -0600)]
[Change] Do not add --phred33-qual option if --no-qualities is enabled

8 years agoThe order of @SQ tags in SAM/BAM files can be arbitrary now
Bo Li [Thu, 9 Feb 2012 00:07:26 +0000 (18:07 -0600)]
The order of @SQ tags in SAM/BAM files can be arbitrary now