Issues · BICF / Astrocyte / atacseq_analysis

New issue

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