chipseq_analysis issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues2021-07-25T17:02:51-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/91Update nf-tower token2021-07-25T17:02:51-05:00Venkat MalladiUpdate nf-tower token2.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/90Strip spaces in design file2020-12-29T17:26:45-06:00Venkat MalladiStrip spaces in design fileStrip leading or trailing spaces in design fileStrip leading or trailing spaces in design file2.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/89Diffbind is tsv not csv2020-12-29T17:23:49-06:00Venkat MalladiDiffbind is tsv not csvDiffbind output is actually tsv not csv file forat.Diffbind output is actually tsv not csv file forat.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)2.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/83Unique Experiment check2020-06-23T15:49:10-05:00Venkat MalladiUnique Experiment checkCheck design file for unique experiments and replicates before starting.Check design file for unique experiments and replicates before starting.2.0.0https://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/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/69add checks to determine if fastq files are in proper format and not truncated2020-06-23T15:52:26-05:00Spencer Barnesadd checks to determine if fastq files are in proper format and not truncatedWe can maybe implement this tool:
https://genome.sph.umich.edu/wiki/FastQValidatorWe can maybe implement this tool:
https://genome.sph.umich.edu/wiki/FastQValidator2.0.0https://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/62Filter reads increase memory2020-12-29T17:30:29-06:00Venkat MalladiFilter reads increase memoryIncrease memory allocation upon failure:
https://github.com/nf-core/chipseq/blob/master/conf/base.config
https://www.nextflow.io/docs/latest/process.html?highlight=retryIncrease memory allocation upon failure:
https://github.com/nf-core/chipseq/blob/master/conf/base.config
https://www.nextflow.io/docs/latest/process.html?highlight=retry2.0.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/44diffbind design file error2020-06-23T15:51:25-05:00Spencer Barnesdiffbind design file errorThe step that creates the diffbind design file copies the SampleID column into the Condition column. This causes an error since this causes diffbind to compare N different conditions instead of the expected 2 or 3. Possible fix would cha...The step that creates the diffbind design file copies the SampleID column into the Condition column. This causes an error since this causes diffbind to compare N different conditions instead of the expected 2 or 3. Possible fix would change the diffbind script to compare Factor or Treatment as default.2.0.0Spencer BarnesSpencer Barneshttps://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/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 Malladi