chipseq_analysis issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues2019-05-20T13:01:02-05:00https://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/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/chipseq_analysis/-/issues/17Move to use Process scripts2020-03-20T23:08:02-05:00Venkat MalladiMove to use Process scriptsVenkat 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/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/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/29add plotProfile2020-03-15T12:57:07-05:00Holly Ruessadd plotProfileAdd plotProfile for each sampleAdd plotProfile for each sample1.1.0Jeremy MathewsJeremy Mathewshttps://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/39Optimizations2020-06-23T15:51:07-05:00Jonathan GesellOptimizationsGeneral speed-ups and optimization of pipeline branches.General speed-ups and optimization of pipeline branches.3.0.0Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/45Remove spaces and "weird characters" from design files2019-07-30T09:16:32-05:00Holly RuessRemove spaces and "weird characters" from design files[design.tsv](/uploads/97cb32a15d52c0d7efdff112e1adefd2/design.tsv)
See attached design file. Remove spaces after names and test for weird characters (. - _ ,) to see which programs fail and then remove those at the check design file[design.tsv](/uploads/97cb32a15d52c0d7efdff112e1adefd2/design.tsv)
See attached design file. Remove spaces after names and test for weird characters (. - _ ,) to see which programs fail and then remove those at the check design file1.1.0Jeremy MathewsJeremy Mathews