mauranolab mapping issues

mauranolab / mapping

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bamintersect .bam files missing custom reference reads

#274 mattmaurano closed 1 year ago
0
add analyzeBCargs parameter

#273 andremrsantos closed 2 years ago
9
add filters to trackhub

#272 andremrsantos closed 2 years ago
0
sort Flowcell tracks by date rather than by category

#271 mattmaurano opened 2 years ago
0
provide better checkboxes for By_Locus and Flowcell tracks

#270 mattmaurano opened 2 years ago
0
MakeTrackhub.py compatible with updated trackhub

#269 andremrsantos closed 2 years ago
1
yeast mappings for yeast/mammalian mappings not visible in track hub

#268 mattmaurano opened 2 years ago
0
Add GC Bias plot to analyze insert

#267 andremrsantos closed 3 years ago
0
Color bigBed tracks by strand

#266 mattmaurano closed 2 years ago
2
Enable filtering

#265 mattmaurano closed 2 years ago
14
Merge in latest daler/trackhub

#264 mattmaurano closed 2 years ago
8
clean up bcftools indexing and bgzip output

#263 mattmaurano closed 3 years ago
0
add pruneLowJaccard filter to genotypeClones.py

#262 andremrsantos closed 3 years ago
0
Added delly to the pipeline.

#261 MarkGrivainis closed 3 years ago
0
Update genotypeClones parameters

#260 andremrsantos closed 3 years ago
10
Miss typed parameter

#259 andremrsantos closed 3 years ago
0
genotypeClones improvement

#258 andremrsantos closed 3 years ago
0
Output clone transfection

#257 andremrsantos closed 3 years ago
4
fix analyzeIntegrations.sh bug that prevent selection of single-site

#256 andremrsantos closed 3 years ago
0
Add configurable parameters to mapIntegrations.sh

#255 andremrsantos closed 3 years ago
3
add check if noBC length and skip check

#254 andremrsantos closed 3 years ago
0
Add code for the new t2t genome

#253 cadley-nyulangone closed 3 years ago
0
SpeedUp AdjacencyDeDup.py

#252 andremrsantos closed 3 years ago
13
Adjust MakeTrackhub.py to read 9 columns from bb files.

#251 cadley-nyulangone closed 3 years ago
0
Color genotypes bb lines

#250 cadley-nyulangone closed 3 years ago
5
Add no bc support to ipcr mapping

#249 andremrsantos closed 3 years ago
1
Add an Analysis column to the counts.txt output files

#248 cadley-nyulangone closed 3 years ago
2
Move calculation of num_bam1_reads

#247 cadley-nyulangone closed 3 years ago
0
Add new column to all .counts.txt output files

#246 mattmaurano closed 3 years ago
0
benchmark read counting bottleneck step

#245 mattmaurano closed 3 years ago
4
Missing HTML summary table

#244 mattmaurano closed 3 years ago
8
Generate bb bw and vcf files when there are no reads in the bam file

#243 cadley-nyulangone closed 3 years ago
5
Add talOcc4 to CEGS_genomes

#242 cadley-nyulangone closed 3 years ago
1
Add talOcc4 to CEGS_genomes

#241 cadley-nyulangone closed 3 years ago
4
Make empty bb and bw files for zero analyzedReads

#240 cadley-nyulangone closed 3 years ago
8
add t2t to genomeinfo.sh

#239 ramoya closed 3 years ago
0
fixPruneConflictNodesBug

#238 andremrsantos closed 3 years ago
0
Add remove conflicting BCs

#237 andremrsantos closed 3 years ago
0
useAnalyticBridgeCentrality

#236 andremrsantos closed 3 years ago
0
fixT0190AnalyzeBCCountsBUG

#235 andremrsantos closed 3 years ago
2
speed-up filterNodesFromFile

#234 andremrsantos closed 3 years ago
7
Genotype clones fixes

#233 andremrsantos closed 3 years ago
0
Add curly braces around dnase pipeline shell input parameter numbers

#232 cadley-nyulangone closed 3 years ago
0
Add curly braces around all bamintersect shell input parameter numbers.

#231 cadley-nyulangone closed 3 years ago
0
Permit passing separate bam file to count reads for normalization

#230 cadley-nyulangone closed 3 years ago
5
breakUpWeaklyConnectedCommunities speed-up

#229 andremrsantos closed 3 years ago
0
Permit passing separate bam file to count reads for normalization

#228 mattmaurano closed 3 years ago
0
genotypeClones speedup

#227 andremrsantos closed 3 years ago
1
fix genotypeClones update bugs

#226 andremrsantos closed 3 years ago
0
New post genotypeClones.py clean-up interface proposal

#225 andremrsantos closed 3 years ago
1