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atacseq_analysis
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  • Astrocyte
  • atacseq_analysis
  • Issues

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