chipseq_analysis issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues2019-01-06T09:22:05-06:00https://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/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/10Add in grouping variable2017-10-11T13:35:05-05:00Venkat MalladiAdd in grouping variableAdd in grouping variable experiment_idAdd in grouping variable experiment_id1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/7Add in Macs2 support2017-11-20T12:14:00-06:00Venkat MalladiAdd in Macs2 supportAdd in Macs2 support for calling Peaks for Histone Data.
Also add signal generation step.Add in Macs2 support for calling Peaks for Histone Data.
Also add signal generation step.1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/3Add mapping and trimming2017-10-11T09:06:35-05:00Venkat MalladiAdd mapping and trimmingAdd in mapping and trimming stepsAdd in mapping and trimming steps1.0.0Venkat MalladiVenkat Malladihttps://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/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/4Bam Stats and Filter2017-10-11T09:06:48-05:00Venkat MalladiBam Stats and FilterFilter bam for duplications and calculate bam statsFilter bam for duplications and calculate bam stats1.0.0Venkat 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/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/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/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/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/5Include Phantompeakqualtools step2017-10-24T21:02:23-05:00Venkat MalladiInclude Phantompeakqualtools stepAdd in [Phantompeakqualtools](https://github.com/kundajelab/phantompeakqualtools)
Use phantompeakqualtools to get
NSC
RSC
est_frag_lenAdd in [Phantompeakqualtools](https://github.com/kundajelab/phantompeakqualtools)
Use phantompeakqualtools to get
NSC
RSC
est_frag_len1.0.0Venkat 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/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/38Missing modules2019-04-23T07:48:40-05:00Venkat MalladiMissing modules1.0.0Venkat 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/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/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 Malladi