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BushmanLab
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intSiteCaller
GNU General Public License v3.0
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Error "Can't open NA.2bit to read"
#75
sejjbia
opened
4 years ago
3
Modified get_reference_genome to drop alt seqs.
#74
cnobles
closed
6 years ago
0
Replace actual quality trimming.
#73
cnobles
opened
6 years ago
0
Demultiplex Update
#72
cnobles
closed
6 years ago
0
callSites-Recode
#71
cnobles
closed
7 years ago
0
Revert "callSites-Recode"
#70
cnobles
closed
7 years ago
0
callSites-Recode
#69
cnobles
closed
7 years ago
0
callSites-Recode
#68
cnobles
closed
7 years ago
0
Trim and align fix
#67
cnobles
closed
7 years ago
0
Trim and align fix
#66
cnobles
closed
7 years ago
0
Miscalling integration site and breakpoint positions on genome
#65
cnobles
opened
7 years ago
1
Qsub
#64
helixscript
closed
8 years ago
0
counts in sites.final do not accurately represent the number of reads
#63
cnobles
closed
8 years ago
0
PrimerID reporting is broken
#62
cnobles
closed
8 years ago
1
U3seq
#61
cnobles
closed
7 years ago
0
Additional checks for read pairing
#60
cnobles
closed
8 years ago
0
R2 filter adjustment
#59
cnobles
closed
8 years ago
0
Multihit clustering
#58
cnobles
closed
8 years ago
1
if genome is not installed need to halt immediately and write message to user
#57
anatolydryga
opened
8 years ago
0
Trim
#56
anatolydryga
closed
8 years ago
0
pairing needs to understand down stream
#55
yhwu
closed
8 years ago
1
High memory usage
#54
yhwu
closed
8 years ago
1
Consider using rep() in line 68 of code review code
#53
kylebittinger
closed
8 years ago
0
Print all sample
#52
yhwu
closed
8 years ago
0
LSF system stall if alignSeqs not sucessful
#51
yhwu
opened
8 years ago
0
JobID error intSiteCallerJob[1-0]
#50
yhwu
closed
8 years ago
0
Register metadata with Bushman Registry
#49
aubreybailey
opened
9 years ago
3
ignore primerIDData md5's, they are not used in the pipeline at the m…
#48
yhwu
closed
9 years ago
0
add accuracy test
#47
yhwu
opened
9 years ago
0
reduced memory usage for multihit clustering by condensing identical …
#46
esherm
closed
9 years ago
0
test_identical_run.R fails
#45
anatolydryga
closed
9 years ago
0
what do we do with identical reads?
#44
anatolydryga
closed
8 years ago
0
test hangs if new job is created after script is started
#43
anatolydryga
closed
9 years ago
1
should we remove suppressWarnings? from everywhere
#42
anatolydryga
opened
9 years ago
0
parallel demultiplexing
#41
anatolydryga
closed
9 years ago
1
on the top level we only want to have run scripts(everything else should be hidden in folder)
#40
anatolydryga
opened
9 years ago
0
Bsub array limit
#39
yhwu
closed
9 years ago
1
bsub cannot submit array job with too many subjobs
#38
yhwu
closed
9 years ago
0
Calc multihit last
#37
yhwu
closed
9 years ago
0
Correcting barcode results in 20% loss of reads. Too much.
#36
yhwu
closed
9 years ago
4
Demultiplex same barcode
#35
yhwu
closed
9 years ago
0
Cleanfolder
#34
yhwu
closed
9 years ago
1
Checksampleexistindb
#33
yhwu
closed
9 years ago
0
Modify standardized sites
#32
yhwu
closed
9 years ago
0
should we use clustering or reduce
#31
anatolydryga
closed
9 years ago
0
Dereplicating and Clustering sites may result in up stream shift of 5bp or more.
#30
yhwu
closed
9 years ago
1
check_stats.R crashes on unfinished run
#29
cnobles
closed
9 years ago
6
***samples with two refGenome
#28
yhwu
closed
9 years ago
1
***deal with re-dos on the same GTSPs
#27
yhwu
closed
9 years ago
3
***top priority, UninfectedControls-1, names for control should have runid in it,
#26
yhwu
closed
9 years ago
3
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