chipseq_analysis issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues2019-01-06T09:21:11-06:00https://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/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/20invalid option in map_qc.py2019-01-05T22:37:45-06:00Spencer Barnesinvalid option in map_qc.pyLine 190:
"samtools index -@ %d %s" % (cpu_count(), final_bam_filename)
Error thrown that '-@' in an invalid option. Samtools v1.6 manual confirms this is not a valid option for 'samtools index'. Testing whether removing this opti...Line 190:
"samtools index -@ %d %s" % (cpu_count(), final_bam_filename)
Error thrown that '-@' in an invalid option. Samtools v1.6 manual confirms this is not a valid option for 'samtools index'. Testing whether removing this option throws additional errors.https://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/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/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/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/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/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/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/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 Malladi