BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2019-01-11T10:48:11-06:00https://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 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/8Update documentation2019-05-06T11:13:09-05:00Venkat MalladiUpdate documentation1.0.0Holly RuessHolly Ruesshttps://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/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/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/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/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/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