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NCI-CGR
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IlluminaSequencingAnalysis
All Illumina Sequencing Related project from Xin will be recorded in this repo
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H-Pylori: Obtain Methylation Info in both Gene and Ref
#60
lxwgcool
opened
8 months ago
0
New Ad-hoc requirement: Prepare KIR region for COVID WGS BAM
#59
lxwgcool
opened
10 months ago
2
New Project: find ecotypes from HKBC gene expression dataset
#58
lxwgcool
opened
1 year ago
0
H-pylori: Generate BAM for 1000+ samples by using 4 different reference
#57
lxwgcool
opened
1 year ago
10
Ad-hoc: H Pylori Project Call variant by using assembled sample
#56
lxwgcool
opened
1 year ago
1
Ad-hoc: Prepare the sliced BAMs for Cenk's group (TCR loci and IGK.)
#55
lxwgcool
opened
1 year ago
0
Prepare
#54
lxwgcool
opened
1 year ago
0
Discussion: BWA performance evaluation (different number of computational resources)
#53
lxwgcool
opened
1 year ago
4
Debug: bad demultiplxing
#52
lxwgcool
opened
2 years ago
0
Ad-hoc Requirement: from Cenk
#51
lxwgcool
opened
2 years ago
7
COVID 19 project: Multiple changes and modifications
#50
lxwgcool
opened
2 years ago
0
COVID_Project: Change the name of some directory to make it easy to be read
#49
lxwgcool
opened
2 years ago
1
COVID_2nd_pipeline: stop when some run occurred
#48
lxwgcool
opened
2 years ago
0
COVID_Auto_Framework: Several New features
#47
lxwgcool
opened
2 years ago
2
COVID_Auto_Framework: Add Email Notification
#46
lxwgcool
opened
2 years ago
1
Fix the bug of missing flags for some subject; New functions of parallel computing and some additional issues
#45
lxwgcool
opened
2 years ago
2
COVID Project: Back up post-primary-analysis data from biowulf to S3
#44
lxwgcool
opened
2 years ago
1
Customized QC: New tool: CombineReport
#43
lxwgcool
opened
2 years ago
1
COVID Project: Multiple updates for the code based on bad report
#42
lxwgcool
opened
2 years ago
2
COVID_Auto_Framework: fix the bug of pre-calling-qc-report
#41
lxwgcool
opened
2 years ago
0
COVID project (all three): transfer from v37 to v38, and WES to WGS
#40
lxwgcool
opened
2 years ago
0
COVID_Auto_Framework: Automatic framework for COVID project
#39
lxwgcool
opened
2 years ago
0
CustomizedQC: retrieve sample from S3 based on keytable
#38
lxwgcool
opened
2 years ago
1
COVID_2nd_Pipeline: the essential code from 2nd pipeline that be used for COVID project
#37
lxwgcool
opened
2 years ago
3
CustomizedQC: Add testing dataset
#36
lxwgcool
opened
2 years ago
1
Costumized QC: Add new features for MergeSample and BAM Contamination
#35
lxwgcool
opened
2 years ago
0
CustomizedQC: Add new function "Merge Sample"
#34
lxwgcool
opened
2 years ago
1
Tools: Compare the similarity between UCSC v38 bed file and UCSC hg19 bed file
#33
lxwgcool
opened
2 years ago
2
Tools: New tools to merge the overlapped region in Bed file together
#32
lxwgcool
opened
2 years ago
0
NovoAlign VS BWA
#31
lxwgcool
opened
2 years ago
6
Customized QC: multiple changes for "CustomizedQC.py", " DataReconstruct.py", "MergeQCReport.py" and "Backup2S3.py"
#30
lxwgcool
opened
2 years ago
0
Generate QC report for low input and std input smaples
#29
lxwgcool
opened
2 years ago
0
VCFClassification: need to sort both chromosome and position
#28
lxwgcool
opened
2 years ago
0
Customized QC: Get data from S3 back to network storage system (biowulf)
#27
lxwgcool
opened
2 years ago
1
Customized QC: update the logic of Generating QC Report / Merging QC Report
#26
lxwgcool
opened
2 years ago
0
Customized QC: checkquota error
#25
lxwgcool
opened
2 years ago
4
Customized QC: bug, bacl2s3.py code failed
#24
lxwgcool
opened
2 years ago
1
Auto-decide how many flowcells can be run parallelly
#23
lxwgcool
opened
3 years ago
1
CustomizedQC: Move data from biowulf to object storage system (S3)
#22
lxwgcool
opened
3 years ago
2
CustomizedQC: still have fastq file for a sample distributed in different lanes (more than 1)
#21
lxwgcool
opened
3 years ago
3
CustomizedQC: update the email list for the case of all set
#20
lxwgcool
opened
3 years ago
0
CustomizedQC: failed to rerun failed jobs (alignment)
#19
lxwgcool
opened
3 years ago
1
CustomizedQC: submitted jobs were missing & run 2 batches a time
#18
lxwgcool
opened
3 years ago
0
VCFClassification: Add a new function to sort and remove duplicate lines in VCF
#17
lxwgcool
opened
3 years ago
0
CustomizedQC: failed to delete the merge sample after mapping
#16
lxwgcool
opened
3 years ago
0
CustomizedQC: unexpected warning email "tput: No value for $TERM and no -T specified"
#15
lxwgcool
opened
3 years ago
0
CustomizedQC: Increase the computing resources to accelerate the speed of analysis.
#14
lxwgcool
opened
3 years ago
1
Customized QC: new logic to merge sample first before do alignment
#13
lxwgcool
opened
3 years ago
1
Customized QC: use the majority barcode to name the reads and sample
#12
lxwgcool
opened
3 years ago
1
Customized QC: put the fastq files from the same sample into a single sample folder
#11
lxwgcool
opened
3 years ago
0
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