Astrocyte issueshttps://git.biohpc.swmed.edu/groups/BICF/Astrocyte/-/issues2020-01-02T14:27:29-06:00https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/2deeptools version 3 error2020-01-02T14:27:29-06:00Spencer Barnesdeeptools version 3 errorWhen calculating signal using bamCoverage, deeptools version 3 does not recognize output of filter_reads step as bam files. Deeptools version 2.5.* does work currently.When calculating signal using bamCoverage, deeptools version 3 does not recognize output of filter_reads step as bam files. Deeptools version 2.5.* does work currently.Version 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/3mitochondrial chromosome reads2020-01-02T14:26:27-06:00Spencer Barnesmitochondrial chromosome readsRe-write script to remove mitochondrial reads as an option. We should also get the percentage of mitochondrial reads in all reads.Re-write script to remove mitochondrial reads as an option. We should also get the percentage of mitochondrial reads in all reads.Version 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/4pool and pseudoreplicate2020-01-02T14:24:34-06:00Spencer Barnespool and pseudoreplicatepool_and_pseudoreplicate.py script creates temporary working files which interfere with one another when running various instances in the same directory.pool_and_pseudoreplicate.py script creates temporary working files which interfere with one another when running various instances in the same directory.Version 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/5Re-direct output2020-01-02T14:24:08-06:00Holly RuessRe-direct outputAdd an option to name the output folderAdd an option to name the output folderVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/11Change output from png to pdf2020-01-02T14:23:29-06:00Holly RuessChange output from png to pdfAny graphic that is a *.png needs to be *.pdf
This is for better qualityAny graphic that is a *.png needs to be *.pdf
This is for better qualityVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/36AWSify2020-01-01T11:10:17-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAWSifyv2.1.5Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/18Fix Convert Reads2019-12-27T14:34:30-06:00Holly RuessFix Convert ReadsVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/17Fix Experiment QC2019-12-20T10:28:15-06:00Holly RuessFix Experiment QCVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/15Fix Filter Reads2019-12-18T08:03:54-06:00Holly RuessFix Filter ReadsVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/16Fix Align Reads2019-12-16T17:14:34-06:00Holly RuessFix Align ReadsVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/14Fix Trim Reads2019-12-11T08:23:17-06:00Holly RuessFix Trim ReadsMake corrections to Trim ReadsMake corrections to Trim ReadsVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/13update check design file2019-12-09T13:27:55-06:00Holly Ruessupdate check design fileUpdate check design file and add seq lengthUpdate check design file and add seq lengthVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/12Remove unnecessary columns from design file2019-12-04T08:53:16-06:00Holly RuessRemove unnecessary columns from design fileDesign file is the same as chip-seq. Some columns are never used, so we should just remove themDesign file is the same as chip-seq. Some columns are never used, so we should just remove themVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/10Update script to incorrpoarte chagnes from ChiP_seq pipeline2019-12-03T10:27:14-06:00Venkat MalladiUpdate script to incorrpoarte chagnes from ChiP_seq pipelineUpdate scripts to include changes to sample names and outputfolderUpdate scripts to include changes to sample names and outputfolderVersion 1.0Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/8Make ATAC-seq pipeline generalizibe for Open Chromatin2019-12-03T10:26:25-06:00Venkat MalladiMake ATAC-seq pipeline generalizibe for Open ChromatinVersion 1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/35Cleanup process outputs2019-11-08T10:30:03-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduCleanup process outputsv2.1.5Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/37Check for space in design file error2019-11-07T16:50:49-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduCheck for space in design file errorSee cellranger_mkfastq#31See cellranger_mkfastq#31v2.1.1Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/34add checks to checkDesign process2019-11-07T12:44:19-06:00Spencer Barnesadd checks to checkDesign processAdd checks to make sure there are no spaces or extra lines in design file.Add checks to make sure there are no spaces or extra lines in design file.v2.1.5Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/33Untar folder structure2019-09-11T10:46:24-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduUntar folder structureMcDermott sequencing core usually tar's just the folder which contains the bcl files... occasionally they include it in a bunch of sub folders.
After untaring... we need to remove those unnecessary parent folders... I would look for the...McDermott sequencing core usually tar's just the folder which contains the bcl files... occasionally they include it in a bunch of sub folders.
After untaring... we need to remove those unnecessary parent folders... I would look for the RTAComplete.txt and if not in just 1 folder... then move the containing folder to to be the root of the process... OR find a way for the process output just to output that parent dirv2.1.5Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/9Update to bicfbase:1.12019-09-10T16:28:20-05:00Jonathan GesellUpdate to bicfbase:1.1Update to use the proper Docker images from the repo.Update to use the proper Docker images from the repo.Jonathan GesellJonathan Gesell