JaneliaSciComp msg issues

JaneliaSciComp / msg

Multiplexed Shotgun Genotyping

http://genomics.princeton.edu/AndolfattoLab/MSG.html

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issues

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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