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deweylab
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RSEM
RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
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RSEM reporting zero transcripts in RSEM references during `calculate-expression`, despite `prepare-references` showing correct number
#167
acesnik
closed
3 years ago
1
RSEM uses the supplied prefix differently for RSEM output files vs STAR intermediate output files
#166
RamRS
opened
3 years ago
1
RSEM calculate expression doesn't work
#165
drumcoco
opened
3 years ago
1
The minimum value of TPM is 0,and the second smallest value is 0.01
#164
Gaodelike
closed
1 year ago
0
STAR errors out asking for a specific parameter
#163
RamRS
closed
3 years ago
3
Compile on Mac
#162
ghost
opened
3 years ago
2
Documentation pages links = Error 404
#161
pcgturrini
opened
3 years ago
4
The index file cannot generate.
#160
chief-wang
opened
3 years ago
0
Fix typo in error message
#159
nh13
opened
3 years ago
0
One of the mate is not paired-end!
#158
MoLuLuMo
opened
3 years ago
1
Error in Prep Reference and Calculating Expression
#157
mh425
opened
3 years ago
0
Estimate expression from pre-computed STAR alignments
#156
MoLuLuMo
opened
3 years ago
2
Issue when calculating expression with RSEM 1.3.3
#155
necrosnake91
closed
3 years ago
2
IsoPct
#154
mhjiang97
closed
3 years ago
1
RSEM 1.3.3 reports wrong version number
#153
Shellfishgene
opened
3 years ago
1
rename in rsem-calculate-expression throws "Invalid cross-device link"
#152
nitishnih
opened
3 years ago
0
One of the shortest noncoding transcript is the most abundant according to rsem-calculate-expression
#151
kaltinel
opened
3 years ago
1
How to visualize transcript-coordinate bam in IGV?
#150
wendy517
closed
3 years ago
0
Some reads do not map the proper transcript...? Index of transcripts corrupted?
#149
aalvarezf
opened
3 years ago
1
Running with strandedness fails on rsem-tbam2gbam to produce output-genome bam
#148
akmorrow13
opened
3 years ago
0
RSEM: WARNING: --genomeSAindexNbases 14 is too large for the genome size=375049285, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 13
#147
Rohit-Satyam
opened
3 years ago
2
warning!!!!aligner you use gave different read lengths for a same read in SAM file
#146
shelfey
opened
3 years ago
2
rsem-simulate-reads in RSEM 1.3.3
#145
mhjiang97
opened
3 years ago
6
Running STAR separately
#144
czfoo
opened
3 years ago
1
The SAM/BAM file declares more reference sequences (572504) than RSEM knows (88647)!
#143
LHXqwq
opened
3 years ago
8
rsem-prepare-reference error
#142
qicaibiology
closed
3 years ago
0
RSEM 1.3.3 reports version as 1.3.1
#141
jergosh
closed
4 years ago
0
issues with command options
#140
lvweiming
closed
2 years ago
0
Reporting incorrect version
#139
rdavison
opened
4 years ago
0
Error while using RSEM in trinity pipeline
#138
bioinfonext
opened
4 years ago
0
Prep Reference Issues
#137
pthom010
opened
4 years ago
1
two mates are aligned to two different transcripts!
#136
snijesh
opened
4 years ago
6
Star Index Out of Ram Issue
#135
mbcouger
opened
4 years ago
3
RSEM 1.3.3 fails at rsem-calculate-credibility-intervals
#134
kelenhiik
opened
4 years ago
4
Error: #two mates are aligned to two different transcripts!
#133
Rohit-Satyam
opened
4 years ago
0
Extra "}" in `rsem-prepare-reference`
#132
kmnip
closed
4 years ago
1
cnt_file total number of reads
#131
qoiopipq
closed
4 years ago
3
Count Positive But TPM and FPKM Are Zero
#130
DarioS
opened
4 years ago
1
rsem-run-ebseq error
#129
guptapa
opened
4 years ago
0
make pRSEM fails on CentOS 7
#128
mathog
opened
4 years ago
1
rsem-calculate-expression and dovetail alignments
#127
sckb
opened
4 years ago
1
rsem-calculate-expression on paired-data. Problems with mate1 and mate2
#126
jonasungerback
opened
4 years ago
1
Issue with RSEM-calculate-expression.. No
#125
hyunjunkang
opened
4 years ago
1
Please port to Python3
#124
tillea
opened
4 years ago
0
rsem calculate expression error
#123
ssri28
opened
4 years ago
0
inconsistent results of rsem quantification
#122
gnilihzeux
opened
5 years ago
0
Conda RSEM + DETONATE
#121
lmfaber
opened
5 years ago
0
Necessity of Preparing Reference if BAM Files Input
#120
DarioS
opened
5 years ago
0
rsem-for-ebseq-calculate-clustering-info not found through conda installation
#119
yifangt
opened
5 years ago
4
How to deal with BAM with gapped alignments?
#118
sammyjava
opened
5 years ago
3
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