BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2020-04-16T22:22:58-05:00https://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 Malladihttps://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/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/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/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/6Update deeptools2017-10-18T17:22:39-05:00Venkat MalladiUpdate deeptoolsUpdate current deeptools step to incorporate into pipelineUpdate current deeptools step to incorporate into pipeline1.0.0Venkat 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/8Update documentation2019-05-06T11:13:09-05:00Venkat MalladiUpdate documentation1.0.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/9Add in blacklist2020-06-23T15:50:34-05:00Venkat MalladiAdd in blacklistAdd blacklist support for mm9,mm10,hg19,hg38Add blacklist support for mm9,mm10,hg19,hg382.0.0Venkat 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/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 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/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/14Add in peak call with SPP and IDR2020-06-23T15:50:40-05:00Venkat MalladiAdd in peak call with SPP and IDR2.0.0Venkat 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/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/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/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/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/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 Luo