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JaneliaSciComp
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msg
Multiplexed Shotgun Genotyping
http://genomics.princeton.edu/AndolfattoLab/MSG.html
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Add support for paired-end read alignment
#47
fdchevalier
closed
2 years ago
1
MSG can't process paired-end sequences
#46
fdchevalier
closed
2 years ago
0
Solve CSV field error
#45
fdchevalier
opened
2 years ago
4
get_sample_data.sh file locations have changed
#44
pmcarlton
closed
2 years ago
0
Master
#43
dstern
closed
7 years ago
0
Compilation of simple fixes and first attempt at BWA-MEM support
#42
YourePrettyGood
closed
7 years ago
8
add msg.cfg parameter for one.sit.per.read in fit-hmm.R
#41
gregpinero
opened
10 years ago
0
revert pre-theta
#40
dstern
closed
10 years ago
0
Have MSG Log all version numbers of dependencies
#39
gregpinero
opened
11 years ago
0
summaryPlots.R - Single Individual Fix
#38
gregpinero
opened
11 years ago
0
Parsing config files - skip over blank values
#37
gregpinero
opened
11 years ago
0
/ Character in FASTA sequence identifiers causes MSG to think references are directories
#36
gregpinero
opened
11 years ago
2
Viterbi HMM
#35
shackett
opened
11 years ago
17
summaryPlots.R - Generate Off-diagonal LOD on Thinned Data instead of full data
#34
gregpinero
opened
12 years ago
0
MSG incorrectly skips generating stampy index files for indiv's on some reruns
#33
gregpinero
opened
12 years ago
0
Handle slashes (and other chars) in barcodes
#32
gregpinero
opened
12 years ago
0
Parsing - If an individual has no reads, produce error message and continue instead of dying.
#31
gregpinero
closed
12 years ago
1
summaryPlots.R - On memory error in thinning - should show helpful message
#30
gregpinero
opened
12 years ago
0
Don't quality trim files if a trimmed file is already present
#29
gregpinero
closed
12 years ago
0
Fix Stampy Issue: stampy: Error: invalid data stream - and remove ln -s workaround
#28
gregpinero
opened
12 years ago
0
Create more documentation - see notes
#27
gregpinero
opened
12 years ago
0
Remove poor quality reads from fastq file right away using TQSfastq.py
#26
gregpinero
closed
12 years ago
3
Samtools location
#25
lparsons
opened
12 years ago
7
Create a new tag, and figure out best way to include release/tag # in MSG
#24
gregpinero
closed
12 years ago
0
Include More Dependencies in Source/GitHub
#23
gregpinero
opened
12 years ago
0
Change Perl Modules to use strict mode
#22
gregpinero
opened
12 years ago
0
msg.pl - updating genomes step - samtools view command references missing var
#21
gregpinero
closed
12 years ago
1
Parse gzipped fastq files directly
#20
gregpinero
closed
12 years ago
0
extract ref alleles - dynamically set low memory mode based on input file size and avail. memory
#19
gregpinero
closed
12 years ago
1
If extract_ref_alleles finds no references, it should die w/ useful error, con't pipeline w/ orig. genome
#18
gregpinero
opened
12 years ago
0
Update Code with Tina's changes
#17
JaneliaSciComp
closed
12 years ago
0
Add verbosity option for data output
#16
gregpinero
closed
12 years ago
1
Make code run faster
#15
gregpinero
closed
12 years ago
0
Investigate and Fix Strange Error Message
#14
gregpinero
opened
12 years ago
0
Validate that all output files were created
#13
gregpinero
closed
12 years ago
0
fit-hmm.R make maximum number of reads a parameter passed in from msg.cfg
#12
gregpinero
opened
12 years ago
0
Investigate (and possibly fix) source of stochasticity
#11
gregpinero
closed
12 years ago
0
Github - Set up release tags
#10
gregpinero
closed
12 years ago
0
min_coverage parameter is not read from msg.cfg
#9
gregpinero
closed
12 years ago
0
Other MSG repos: Take down, or put up note that this is master repo
#8
JaneliaSciComp
opened
12 years ago
0
Feature: change code to use max_coverage
#7
JaneliaSciComp
closed
12 years ago
0
feature: msgRun1.sh doesn't need to wait can be in parallel
#6
JaneliaSciComp
closed
12 years ago
2
Change email for login for JanaliaSciComp user to something generic for Janelia
#5
JaneliaSciComp
opened
12 years ago
0
Feature: Clean up un-needed intermediate data files after run
#4
JaneliaSciComp
closed
12 years ago
0
Bug: Don't require blank line on last line of barcodes file
#3
JaneliaSciComp
closed
12 years ago
2
Bug: allow spaces around = in msg.cfg
#2
JaneliaSciComp
closed
12 years ago
0
Bring in pull requests from tinathu/msg
#1
JaneliaSciComp
closed
12 years ago
1