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blahah
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transrate
Understand your transcriptome assembly
http://hibberdlab.com/transrate
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Consider replacing eXpress with Salmon
#104
blahah
closed
9 years ago
8
Bowtie
#103
blahah
closed
10 years ago
8
Optimal score cutoff selection
#102
blahah
closed
9 years ago
4
Proper read pairing
#101
cboursnell
closed
10 years ago
0
Proper reads pairs
#100
cboursnell
closed
10 years ago
9
hide the --profile option
#99
blahah
closed
10 years ago
0
crash during bam-read
#98
macmanes
closed
10 years ago
3
More explicit logging with debug option
#97
blahah
closed
8 years ago
2
samtools sort flag
#96
macmanes
closed
10 years ago
4
Require latest version of bam-read
#95
cboursnell
closed
10 years ago
0
timestamp with [ INFO]
#94
macmanes
closed
10 years ago
2
print help message when run with no arguments
#93
blahah
closed
10 years ago
0
Small fixes
#92
cboursnell
closed
10 years ago
2
merge cbournsell branch
#91
blahah
closed
10 years ago
0
use SNAP aligner
#90
blahah
closed
10 years ago
0
Actual read length used for effective length calculations
#89
cboursnell
closed
10 years ago
1
Calculate read length to use for effective length calculations
#88
cboursnell
closed
10 years ago
4
Massive speed up of bcf file parsing using C
#87
cboursnell
closed
10 years ago
1
can't find Bowtie2, even though it exists.
#86
macmanes
closed
10 years ago
2
Singleton
#85
MatthewRalston
closed
8 years ago
1
Stranded
#84
MatthewRalston
closed
8 years ago
5
Genome
#83
MatthewRalston
closed
8 years ago
1
Blast runtime error in computing comparative metrics
#82
hyundoo
closed
9 years ago
3
Check for existence of files before running samtools commands
#81
cboursnell
closed
10 years ago
3
Fixed problem with edit distance and reference coverage
#80
cboursnell
closed
10 years ago
0
samtools binary download and reference coverage calculation
#79
cboursnell
closed
10 years ago
0
visualisation of assembly metrics
#78
blahah
opened
10 years ago
0
This seems a lot larger than I thought it would be
#77
cboursnell
closed
10 years ago
0
Edit distance and mapq score metrics
#76
cboursnell
closed
10 years ago
2
segmentation of coverage/mapQ signals
#75
blahah
closed
10 years ago
2
use sorted, indexed bam for read metrics
#74
blahah
closed
10 years ago
1
'Loading reference dataset' printed when no reference provided
#73
blahah
closed
9 years ago
0
Everything ready for next release
#72
cboursnell
closed
10 years ago
1
edit distance
#71
blahah
closed
10 years ago
1
variance of expression on a contig
#70
blahah
closed
10 years ago
1
mapq based statistics
#69
blahah
closed
10 years ago
3
Chimera tag
#68
cboursnell
closed
10 years ago
1
problems with 'which' dependency in sudo-installations
#67
blahah
closed
10 years ago
0
Changed metric names to match docs and fix skew calculations
#66
cboursnell
closed
10 years ago
3
Unpaired
#65
MatthewRalston
closed
8 years ago
2
Strand specific option for read alignment
#64
MatthewRalston
opened
10 years ago
0
Fixed the comparative metric tests
#63
cboursnell
closed
10 years ago
1
Replaced inline C with C extension
#62
cboursnell
closed
10 years ago
1
First pull request: --genome feature, --unpaired feature [incomplete]
#61
MatthewRalston
closed
10 years ago
15
Raise error on bowtie2 failure
#60
cboursnell
closed
10 years ago
0
handle bases other than ACTGN in base composition
#59
blahah
closed
10 years ago
0
cli: --print-commands
#58
blahah
closed
8 years ago
3
Parse samtools mpileup chromosome name with BioRuby FastaDefline parser
#57
blahah
closed
10 years ago
1
Add single-read support to read-metrics
#56
blahah
opened
10 years ago
5
Bowtie alignment fails
#55
MatthewRalston
closed
9 years ago
4
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