BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2018-12-16T23:28:02-06:00https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/16Fix Unreplicated experiment naive overlap2018-12-16T23:28:02-06:00Venkat MalladiFix Unreplicated experiment naive overlapFix code for naive overlap codeFix code for naive overlap codeVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/6Genearte Signal Tracks2018-04-10T16:27:31-05:00Venkat MalladiGenearte Signal TracksGenerate Signal Tracks for Vizualization in Browser. (Can use deeptools)Generate Signal Tracks for Vizualization in Browser. (Can use deeptools)https://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/5Deeptools QC metics between samples2018-04-10T16:26:53-05:00Venkat MalladiDeeptools QC metics between samplesPlot Spearman Correlation between samples using Deeptools:
http://deeptools.readthedocs.io/en/latest/content/tools/plotCorrelation.htmlPlot Spearman Correlation between samples using Deeptools:
http://deeptools.readthedocs.io/en/latest/content/tools/plotCorrelation.htmlDanni LuoDanni Luohttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/4RNASeq Pathway Analysis Mouse support2018-04-10T16:21:07-05:00Venkat MalladiRNASeq Pathway Analysis Mouse supportCurrently the workflow doesn't work for mouse genesets -- probably an error in the qusage code in dea.R -- see geneset files in:
/project/shared/bicf_workflow_ref/GRCm38/gsea_gmt/Currently the workflow doesn't work for mouse genesets -- probably an error in the qusage code in dea.R -- see geneset files in:
/project/shared/bicf_workflow_ref/GRCm38/gsea_gmt/Danni LuoDanni Luohttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/3Update RNASeq Shiny Code2018-11-19T11:11:41-06:00Venkat MalladiUpdate RNASeq Shiny Code1) Add ability to download QuSAGE output table (pathway analysis)
2) Heatmap with no sample clustering1) Add ability to download QuSAGE output table (pathway analysis)
2) Heatmap with no sample clusteringDanni LuoDanni Luohttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/2RNASeq New Isoform Detection2021-04-13T12:31:57-05:00Brandi CantarelRNASeq New Isoform DetectionDevelop a workflow for the detection of Exon Skipping, Intron Inclusion (exon extension).Develop a workflow for the detection of Exon Skipping, Intron Inclusion (exon extension).Danni LuoDanni Luohttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/1star broken2018-04-30T09:57:41-05:00Spencer Barnesstar brokenPipeline fails when running with STAR alignment option. Confirmed on two separate runs with different datasets.Pipeline fails when running with STAR alignment option. Confirmed on two separate runs with different datasets.https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/2Update test data2019-05-20T13:01:02-05:00Venkat MalladiUpdate test dataPossible datasets to include. Substitute some for mouse to test in each scenario.
Histone SE: https://www.encodeproject.org/experiments/ENCSR878KIY/
Histone PE: https://www.encodeproject.org/experiments/ENCSR203KEU/
Histone unreplica...Possible datasets to include. Substitute some for mouse to test in each scenario.
Histone SE: https://www.encodeproject.org/experiments/ENCSR878KIY/
Histone PE: https://www.encodeproject.org/experiments/ENCSR203KEU/
Histone unreplicated: https://www.encodeproject.org/experiments/ENCSR368ORV/
TF SE: https://www.encodeproject.org/experiments/ENCSR000DYI/
TF PE: https://www.encodeproject.org/experiments/ENCSR936XTK/
TF Unreplicated: https://www.encodeproject.org/experiments/ENCSR400WEK/
Currently:
TF PE (human): https://www.encodeproject.org/experiments/ENCSR729LGA/
Histone SE (mouse): https://www.encodeproject.org/experiments/ENCSR238SGC/Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/1Add in Fastqc2020-04-16T22:22:58-05:00Venkat MalladiAdd in FastqcAdd in fastqc and testsAdd in fastqc and testsVenkat MalladiVenkat Malladi