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BICF
Astrocyte
atacseq_analysis
Issues
Open
7
Closed
36
All
43
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Manual
Priority
Created date
Updated date
Milestone due date
Due date
Popularity
Label priority
Manual
Title
Weight
Blocking
map_reads failure case
#1
· created
Apr 12, 2018
by
Spencer Barnes
Version 2.1.0
bug
0
updated
Jun 23, 2020
deeptools version 3 error
#2
· created
May 11, 2018
by
Spencer Barnes
Version 2.0
enhancment
CLOSED
1
updated
Jan 02, 2020
mitochondrial chromosome reads
#3
· created
May 11, 2018
by
Spencer Barnes
Version 2.0
critical
CLOSED
0
updated
Jan 02, 2020
pool and pseudoreplicate
#4
· created
May 11, 2018
by
Spencer Barnes
Version 2.0
critical
CLOSED
1
updated
Jan 02, 2020
Re-direct output
#5
· created
Feb 20, 2019
by
Holly Ruess
Version 2.0
critical
CLOSED
0
updated
Jan 02, 2020
Trimming Comparison
#6
· created
Apr 25, 2019
by
Jonathan Gesell
Optimizations
0
updated
Dec 29, 2020
Shift is incorrect for ATAC-seq
#7
· created
May 02, 2019
by
Venkat Malladi
Version 2.0
bug
CLOSED
1
updated
Jan 06, 2020
Make ATAC-seq pipeline generalizibe for Open Chromatin
#8
· created
May 02, 2019
by
Venkat Malladi
Version 1.0
enhancment
CLOSED
1
updated
Dec 03, 2019
Add in references and version used in script
#9
· created
May 02, 2019
by
Venkat Malladi
Version 2.0
critical
CLOSED
1
updated
May 28, 2020
Update script to incorrpoarte chagnes from ChiP_seq pipeline
#10
· created
May 02, 2019
by
Venkat Malladi
Version 1.0
critical
CLOSED
1
updated
Dec 03, 2019
Change output from png to pdf
#11
· created
May 10, 2019
by
Holly Ruess
Version 2.0
enhancment
CLOSED
0
updated
Jan 02, 2020
Remove unnecessary columns from design file
#12
· created
Dec 03, 2019
by
Holly Ruess
Version 2.0
CLOSED
2
0
updated
Dec 04, 2019
update check design file
#13
· created
Dec 06, 2019
by
Holly Ruess
Version 2.0
enhancment
CLOSED
1
0
updated
Dec 09, 2019
Fix Trim Reads
#14
· created
Dec 09, 2019
by
Holly Ruess
Version 2.0
enhancment
CLOSED
4
0
updated
Dec 11, 2019
Fix Filter Reads
#15
· created
Dec 12, 2019
by
Holly Ruess
Version 2.0
enhancment
CLOSED
1
0
updated
Dec 18, 2019
Fix Align Reads
#16
· created
Dec 12, 2019
by
Holly Ruess
Version 2.0
enhancment
CLOSED
1
0
updated
Dec 16, 2019
Fix Experiment QC
#17
· created
Dec 18, 2019
by
Holly Ruess
Version 2.0
enhancment
CLOSED
1
0
updated
Dec 20, 2019
Fix Convert Reads
#18
· created
Dec 18, 2019
by
Holly Ruess
Version 2.0
enhancment
CLOSED
1
0
updated
Dec 27, 2019
Fix cross correlation
#19
· created
Dec 19, 2019
by
Holly Ruess
Version 2.0
enhancment
CLOSED
1
0
updated
Jan 03, 2020
Fix Pool and Pseudoreps
#20
· created
Dec 20, 2019
by
Holly Ruess
Version 2.0
enhancment
CLOSED
1
0
updated
Jan 03, 2020
Fix concurrent runners
#21
· created
Dec 20, 2019
by
Venkat Malladi
CLOSED
4
updated
May 28, 2020
Make hg19 test
#22
· created
Jan 01, 2020
by
Holly Ruess
Version 2.0
enhancment
CLOSED
0
updated
Jan 06, 2020
Fix call peaks MACs
#23
· created
Jan 02, 2020
by
Holly Ruess
Version 2.0
enhancment
CLOSED
1
updated
Jan 07, 2020
fix consensus peaks
#24
· created
Jan 03, 2020
by
Holly Ruess
Version 2.0
enhancment
CLOSED
1
0
updated
Jan 07, 2020
Fix BioHPC config
#25
· created
Jan 06, 2020
by
Holly Ruess
Version 2.0
enhancment
CLOSED
1
0
updated
Jan 07, 2020
Generate MultiQC report
#26
· created
Jan 06, 2020
by
Holly Ruess
Version 2.0
enhancment
CLOSED
1
0
updated
Feb 25, 2020
Add fragment size distribution
#27
· created
Jan 09, 2020
by
Holly Ruess
Version 2.0
enhancment
CLOSED
2
1
updated
Jun 09, 2020
Add percent of reads - mitochondria
#28
· created
Jan 09, 2020
by
Holly Ruess
Version 2.0
enhancment
CLOSED
1
0
updated
Mar 24, 2020
Add FRiP score
#29
· created
Jan 09, 2020
by
Holly Ruess
Version 2.0
enhancment
CLOSED
2
0
updated
May 13, 2020
TSS enrichment score
#30
· created
Jan 09, 2020
by
Holly Ruess
Version 2.0
enhancment
CLOSED
2
0
updated
May 28, 2020
Blacklist of regions
#31
· created
Jan 09, 2020
by
Holly Ruess
Version 2.0
enhancment
CLOSED
1
0
updated
Jun 09, 2020
Annotate peaks
#32
· created
Jan 09, 2020
by
Holly Ruess
Version 2.0
enhancment
CLOSED
1
0
updated
Jun 11, 2020
Motif search in peaks
#33
· created
Jan 09, 2020
by
Holly Ruess
Version 2.1.0
enhancment
0
updated
Jun 23, 2020
Diff Peak analysis
#34
· created
Jan 09, 2020
by
Holly Ruess
Version 2.1.0
enhancment
0
updated
Jun 23, 2020
Change to 256 only if job fails
#35
· created
Jan 09, 2020
by
Holly Ruess
Version 2.1.0
enhancment
0
updated
Jun 23, 2020
update version of nextflow
#36
· created
Feb 26, 2020
by
Holly Ruess
Version 2.1.0
critical
enhancment
0
updated
Jun 23, 2020
Fix runners and sigbus error
#37
· created
Mar 31, 2020
by
Venkat Malladi
CLOSED
1
0
updated
May 08, 2020
Add license
#38
· created
Apr 06, 2020
by
Venkat Malladi
Version 2.0
CLOSED
1
0
updated
May 07, 2020
Tests for astrocyte
#39
· created
Jun 11, 2020
by
Venkat Malladi
CLOSED
1
0
updated
Jun 18, 2020
Astrocyte fixes
#40
· created
Jun 19, 2020
by
Venkat Malladi
CLOSED
1
0
updated
Jun 21, 2020
Update multiqc version/references report
#41
· created
Jun 23, 2020
by
Gervaise Henry
Version 2.1.0
documentation
enhancment
1
0
updated
Jul 01, 2020
Update to astrocyte 0.3.1
#42
· created
Jun 26, 2020
by
Venkat Malladi
Version 2.1.0
CLOSED
0
updated
Jul 01, 2020
map reads fails to make bam files for long reads
#43
· created
Jul 28, 2020
by
Venkat Malladi
bug
critical
CLOSED
1
1
updated
Jul 29, 2020