chipseq_analysis issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues2020-06-23T15:50:34-05:00https://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/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/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/60Make both astrocyte compatable and other cluster compatable2020-06-23T15:51:53-05:00Holly RuessMake both astrocyte compatable and other cluster compatableWe need to move the module load from the main.nf into if astrocyte = True statement.We need to move the module load from the main.nf into if astrocyte = True statement.3.0.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/63Annotate Diffbind output2020-12-29T17:27:14-06:00Holly RuessAnnotate Diffbind outputAnnotate the output of diffBind
use the same annotations as with peak annotations
See Holly for updates on how to use gencode.gtf fileAnnotate the output of diffBind
use the same annotations as with peak annotations
See Holly for updates on how to use gencode.gtf file2.0.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/70Use specific meme file in motif search2020-12-29T17:30:57-06:00Holly RuessUse specific meme file in motif searchDownload meme files from http://meme-suite.org/doc/download.html Motif DB
Add into biohpc config file the correct meme file for each species
Change the meme chip scriptDownload meme files from http://meme-suite.org/doc/download.html Motif DB
Add into biohpc config file the correct meme file for each species
Change the meme chip script2.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/74Annotepeaks2020-06-23T15:49:23-05:00Venkat MalladiAnnotepeaksSeperate annotate peaks with different design file reading to chunk processing so it doesn't read it into memory.Seperate annotate peaks with different design file reading to chunk processing so it doesn't read it into memory.2.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/85Update multiqc version/references report2020-06-23T15:48:58-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate multiqc version/references report* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)2.0.0