chipseq_analysis issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues2019-04-23T07:48:40-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/38Missing modules2019-04-23T07:48:40-05:00Venkat MalladiMissing modules1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/37Fix software versions test2019-04-22T22:30:59-05:00Venkat MalladiFix software versions test1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/36Update Astrocyte documentation and errors2019-04-22T22:18:14-05:00Venkat MalladiUpdate Astrocyte documentation and errors1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/35Fix astrocyte run2019-04-22T15:17:51-05:00Venkat MalladiFix astrocyte runAstrocyte is not using the correct variables in Main.nfAstrocyte is not using the correct variables in Main.nf1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/34Fix tests for software versions2019-04-20T03:12:15-05:00Venkat MalladiFix tests for software versions1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/33New folders for all steps2019-03-16T19:26:26-05:00Venkat MalladiNew folders for all stepsBreak steps into sub-folders by Sample, or Experiment where appropriateBreak steps into sub-folders by Sample, or Experiment where appropriate1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/31skip motif search and diff bind2019-03-12T14:07:41-05:00Holly Ruessskip motif search and diff bindWe don't need to run the analysis all the time. Allow for the skipping of these stepsWe don't need to run the analysis all the time. Allow for the skipping of these steps1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/28Last 3 steps don't go into user defined output directory2019-04-03T08:15:42-05:00Holly RuessLast 3 steps don't go into user defined output directorydiffPeaks, motifSearch, peakAnnotation goes into $baseDir/output even if the output directory is user defined.diffPeaks, motifSearch, peakAnnotation goes into $baseDir/output even if the output directory is user defined.1.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/27Add Pearson correlation, and make Spearman and Pearson Corr Plots pdf2019-01-31T10:27:28-06:00Holly RuessAdd Pearson correlation, and make Spearman and Pearson Corr Plots pdf1.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/25experimentQC plots are empty in PE2019-01-06T09:21:11-06:00Holly RuessexperimentQC plots are empty in PEPE data plots *_fingerprint.png and coverage.png are empty. Works fine for SE dataPE data plots *_fingerprint.png and coverage.png are empty. Works fine for SE data1.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/24Test Astrocyte2019-04-21T11:41:48-05:00Venkat MalladiTest Astrocyte1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/23Use SampleIds/ Experiment Id as file names throughtout pipeline2019-03-10T18:42:13-05:00Venkat MalladiUse SampleIds/ Experiment Id as file names throughtout pipeline1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/22Add defined output folder2019-01-06T09:22:05-06:00Venkat MalladiAdd defined output folder1.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/21Output software versions and methods and references2019-04-18T15:36:36-05:00Venkat MalladiOutput software versions and methods and references1.0.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/19Add multiqc summary of data2019-04-21T12:06:01-05:00Venkat MalladiAdd multiqc summary of data1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/18broken link in documentation2019-01-05T22:41:01-06:00Spencer Barnesbroken link in documentationOn Astrocyte website, link to design file template is broken. Error 404.On Astrocyte website, link to design file template is broken. Error 404.1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/15Add in current chip-analysis functionality.2019-01-11T10:48:11-06:00Venkat MalladiAdd in current chip-analysis functionality.1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/13Pool and Pseudoreplication2017-10-30T23:19:58-05:00Venkat MalladiPool and PseudoreplicationAdd in pooling and pseudoreplication step.
Also add in xcor for psudoreplicates and pooling.Add in pooling and pseudoreplication step.
Also add in xcor for psudoreplicates and pooling.1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/12Make tagAlign files2017-10-23T06:28:35-05:00Venkat MalladiMake tagAlign files1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/11Remove qc_fastq.py2017-10-18T17:25:01-05:00Venkat MalladiRemove qc_fastq.pyRemove unused qc_fastq.py codeRemove unused qc_fastq.py code1.0.0Venkat MalladiVenkat Malladi