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itmat
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rum
RNA-Seq Unified Mapper
http://cbil.upenn.edu/RUM
MIT License
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Create script to generate mapping stats based on final output files
#140
mdelaurentis
opened
11 years ago
0
Usage message for rum2sam omits some required options
#139
mdelaurentis
closed
11 years ago
1
dna mode
#138
greggrant
closed
11 years ago
1
filtering option
#137
e-manduchi
opened
12 years ago
7
sam file slight modification
#136
greggrant
closed
11 years ago
5
Check that all reads.fa.* files were created
#135
mdelaurentis
closed
12 years ago
0
Check that all reads.fa.* files were created
#134
mdelaurentis
closed
11 years ago
0
Fail more gracefully if index is not found
#133
mdelaurentis
closed
11 years ago
0
Unknown option: limit-bowtie-nu
#132
noborujs
closed
12 years ago
2
gzip support
#131
brwnj
closed
11 years ago
2
strand specific feature quantifications problem with header lines
#130
greggrant
closed
12 years ago
1
Paired reads in a single input file are processed as single-end reads
#129
mdelaurentis
closed
12 years ago
0
Configuration failure should clean up the settings directory
#128
delagoya
closed
12 years ago
3
Add field to SAM file
#127
mdelaurentis
closed
11 years ago
1
Out of memory error in quantifyexons.pl
#126
mdelaurentis
closed
12 years ago
2
status needs to be resized
#125
safisher
closed
12 years ago
0
Automatically cleaning up after successful run does not work anymore
#124
khayer
closed
12 years ago
1
Need more feedback at console
#123
safisher
closed
12 years ago
3
Resume / Restart broken?
#122
safisher
closed
12 years ago
4
Reporting many novel exons with the same start or end coordinate
#121
mdelaurentis
opened
12 years ago
0
multi - mapper warning
#120
khayer
closed
12 years ago
7
Remove temporary files during post processing
#119
safisher
opened
12 years ago
0
Don't dump qstat output to error log; use debug log instead
#118
mdelaurentis
closed
12 years ago
1
Change .rum/job_settings parameter location
#117
safisher
closed
12 years ago
3
Quantify novel exons
#116
safisher
closed
12 years ago
6
rum_runner version output doesn't end in a newline character
#115
greggrant
closed
12 years ago
1
make sure rum2sam doesn't crash if RUM_Unique or RUM_NU is empty
#114
greggrant
closed
12 years ago
1
Warning from rum_runner status
#113
mdelaurentis
closed
12 years ago
0
Read length is missing from job_report file
#112
mdelaurentis
closed
12 years ago
0
New 'known' splice-signal to add to junction script
#111
greggrant
closed
12 years ago
0
Differentiate postprocessing log messages from other messages
#110
mdelaurentis
closed
12 years ago
0
Pipe together blat and parsing of output
#109
mdelaurentis
closed
12 years ago
1
Pipe together bowtie and parsing of output
#108
mdelaurentis
closed
12 years ago
1
Make --limit-bowtie-nu the default
#107
mdelaurentis
closed
12 years ago
0
Malformed CIGAR string: 1SM102S
#106
kdaily
opened
12 years ago
14
Fail more gracefully if forward and reverse reads are different sizes
#105
mdelaurentis
closed
12 years ago
1
When tar'ing up log files, don't be verbose
#104
mdelaurentis
closed
12 years ago
0
Malformed CIGAR string
#103
kdaily
closed
12 years ago
1
Problem building index for single annotation source
#102
caofan
closed
12 years ago
6
--notify <email address> flag
#101
delagoya
opened
12 years ago
0
Error with v 2.02_01
#100
e-manduchi
closed
12 years ago
3
updating pig index
#99
e-manduchi
opened
12 years ago
0
post-processing with new gene model
#98
e-manduchi
opened
12 years ago
0
Use of uninitialized value $_ in length at /usr/local/share/perl/5.10.1/RUM/JobReport.pm line 110.
#97
dputhier
closed
12 years ago
2
Unrecognized option --variable-read-lengths
#96
dputhier
closed
12 years ago
2
Make "rum_runner status" indicate if job is actually running
#95
mdelaurentis
closed
12 years ago
0
Changes to user guide
#94
mdelaurentis
closed
12 years ago
1
Not coloring junctions properly
#93
mdelaurentis
closed
12 years ago
1
Make "rum_runner stop" and change "rum_runner kill"
#92
mdelaurentis
closed
12 years ago
1
Track status of preprocessing phase
#91
mdelaurentis
closed
12 years ago
0
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