atacseq_analysis issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues2019-12-27T14:34:30-06:00https://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/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/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/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/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/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/9Add in references and version used in script2020-05-28T13:58:53-05:00Venkat MalladiAdd in references and version used in scriptVersion 2.0Holly RuessHolly Ruesshttps://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/atacseq_analysis/-/issues/7Shift is incorrect for ATAC-seq2020-01-06T13:57:44-06:00Venkat MalladiShift is incorrect for ATAC-seqShift should be switchted in call_peaks_macs2.py
`--shift 73 --extsize %s`
shift 37 and extsize 73Shift should be switchted in call_peaks_macs2.py
`--shift 73 --extsize %s`
shift 37 and extsize 73Version 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/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/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/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 Ruess