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mapping
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fix genotypeClones.py typo
#224
andremrsantos
closed
4 years ago
1
add postCleanUp method interface to genotypeClones
#223
andremrsantos
closed
4 years ago
10
Add support for coloring T0219toT0222
#222
andremrsantos
closed
4 years ago
0
Replace mlr with sort to fix counts_table.sh
#221
cadley-nyulangone
closed
4 years ago
1
Added BC+cellBC saturation curve computation
#220
andremrsantos
closed
4 years ago
0
Normalize reads reported in counts.txt files to reads per 10mm
#219
cadley-nyulangone
closed
4 years ago
4
Add talOcc4 and talOcc4_sacCer3
#218
cadley-nyulangone
closed
4 years ago
0
Normalize read counts by 1M reads
#217
mattmaurano
closed
4 years ago
5
Change bam exclude flags from 3078 to 3076
#216
cadley-nyulangone
closed
4 years ago
0
Color genotype tracks
#215
mattmaurano
closed
3 years ago
13
uninformative reads making it into bam file
#214
mattmaurano
closed
4 years ago
1
Only group reads with same orientation
#213
cadley-nyulangone
closed
4 years ago
0
Only merge reads with same orientation
#212
cadley-nyulangone
closed
4 years ago
0
Make a reference vs chromosomes table for the cegsvectors description…
#211
cadley-nyulangone
closed
4 years ago
0
Fix different UMI cutoff #206
#210
andremrsantos
closed
4 years ago
0
Pos args for merge
#209
cadley-nyulangone
closed
4 years ago
10
Reduce number of callsnps jobs
#208
mattmaurano
closed
4 years ago
0
Avoids a set -u error when range vector is empty, and for loop can be…
#207
cadley-nyulangone
closed
4 years ago
0
Different UMI length cutoff
#206
andremrsantos
closed
4 years ago
3
SARS: default order puts GC content and NCBI genes below track hub
#205
mattmaurano
closed
4 years ago
4
Fix ipcr interrupt
#204
andremrsantos
closed
4 years ago
2
fixInterruptIPCRProcessing
#203
andremrsantos
closed
4 years ago
0
explicit submitMerge.sh module dependencies
#202
andremrsantos
closed
4 years ago
0
add early exit on no read passing filters
#201
andremrsantos
closed
4 years ago
2
fix processed reads weblogo bug
#200
andremrsantos
closed
4 years ago
2
Add pipefail
#199
cadley-nyulangone
closed
4 years ago
0
Add `Number of PE reads` to analyzeIntegrations.sh (#197)
#198
andremrsantos
closed
4 years ago
0
tally number of PE reads for iPCR libraries
#197
mattmaurano
closed
4 years ago
0
Updated Chimeric Rate Naming with iPCR
#196
andremrsantos
closed
4 years ago
0
Select lines from samplesforTrackhub output via mappedgenome, not ann…
#195
cadley-nyulangone
closed
4 years ago
0
error generating bed files under Assemblies
#194
mattmaurano
closed
4 years ago
20
hg38_full mapped genome showing up in cegsvectors
#193
cadley-nyulangone
closed
4 years ago
0
"hg38_full" mapped genome showing up in cegsvectors
#192
mattmaurano
closed
4 years ago
6
Move *_genomes files into assets directories
#191
cadley-nyulangone
closed
4 years ago
4
move *_genomes into assets folders
#190
mattmaurano
closed
4 years ago
0
SAMBLASTER duplicate criteria
#189
mattmaurano
opened
4 years ago
1
Fix no unscaffolded chrom bug on analyzeIntegrations.sh
#188
andremrsantos
closed
4 years ago
0
Fix analyzeIntegration to deal with empty .barcodes.coords.bed files
#187
andremrsantos
closed
4 years ago
0
Revamp trimming
#186
mattmaurano
opened
4 years ago
1
Parallelize generation of more analysis files
#185
mattmaurano
opened
4 years ago
0
Implement macs2 for chipseq broadpeak calling
#184
mattmaurano
opened
4 years ago
0
RNA-seq pipeline
#183
mattmaurano
closed
1 year ago
1
Genotype confirmation for known individuals
#182
mattmaurano
opened
4 years ago
2
Sex confirmation vs. LIMS
#181
mattmaurano
closed
1 year ago
0
automatic contamination scanning
#180
mattmaurano
closed
1 year ago
0
switch @RG parameters to standard key/value interface
#179
mattmaurano
opened
4 years ago
0
Add ability of BLAT to work with CEGS chomosomes
#178
cadley-nyulangone
closed
4 years ago
10
Add fragment length plot below track controls
#177
mattmaurano
closed
4 years ago
3
Update iPCR mapping to use cutadapt to trim adapters
#176
andremrsantos
closed
4 years ago
0
Issue warning for possible duplicate analysis files
#175
cadley-nyulangone
opened
4 years ago
1
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