BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2020-06-23T16:02:34-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/35Change to 256 only if job fails2020-06-23T16:02:34-05:00Holly RuessChange to 256 only if job failsMay need to incorporate maxErrors and maxRetries into processesMay need to incorporate maxErrors and maxRetries into processesVersion 2.1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/34Diff Peak analysis2020-06-23T16:02:40-05:00Holly RuessDiff Peak analysisVersion 2.1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/33Motif search in peaks2020-06-23T16:02:46-05:00Holly RuessMotif search in peaksVersion 2.1.0Holly RuessHolly Ruesshttps://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/KCE/kce_etl/-/issues/25Add tests radiation2019-12-12T08:30:37-06:00Venkat MalladiAdd tests radiationhttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/24Add tests Medication2019-12-12T08:30:26-06:00Venkat MalladiAdd tests Medicationhttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/10File vs Channel2020-08-27T10:18:28-05:00Jeremy MathewsFile vs ChannelCurrently scripts as passed in by channels. try using simple file() command.Currently scripts as passed in by channels. try using simple file() command.Jeremy MathewsJeremy Mathewshttps://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/64Containerization2020-06-23T15:52:34-05:00Jonathan GesellContainerizationContainerize as much of the ChipSeq pipeline as possible, perferably with one container per processContainerize as much of the ChipSeq pipeline as possible, perferably with one container per process3.0.0Jonathan GesellJonathan Gesellhttps://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/cellranger_count/-/issues/35Shiny App2020-08-02T09:57:09-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduShiny App# Shiny app which recreates count's web_summary.html
## Priority 1
* [x] Select dimentionality reduction type
1. PCA
2. tSNE
3. UMAP
* [x] Select clustering type
1. Graph-Based
2. KMeans 2-10
* [x] Plot
* [x] Show DEGs...# Shiny app which recreates count's web_summary.html
## Priority 1
* [x] Select dimentionality reduction type
1. PCA
2. tSNE
3. UMAP
* [x] Select clustering type
1. Graph-Based
2. KMeans 2-10
* [x] Plot
* [x] Show DEGs based on clustering type
## Priority 2
* [ ] Recreate QC page (or find a way to display multi-qc output)
* [ ] Re-calculate Cliff-Knee plot
* Rank order raw_feature_bc_matrix
* Color barcodes from filtered_feature_bc_matrix green... rest redJeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/34Create output plots2020-08-02T09:57:07-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduCreate output plots## output to:
>output/analysis/*/
## plot:
* PCA with graphclust labels
* tSNE with graphclust labels
* UMAP with graphclust labels
## data for plots in:
>output/count*/*/outs/analysis/
#### remember not to try and read the output dir...## output to:
>output/analysis/*/
## plot:
* PCA with graphclust labels
* tSNE with graphclust labels
* UMAP with graphclust labels
## data for plots in:
>output/count*/*/outs/analysis/
#### remember not to try and read the output dir for the input of the new process... instead in the counts processes add the files necessary to a new outputhttps://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/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/KCE/kce_etl/-/issues/16Genomics inventory2020-07-01T20:02:54-05:00Venkat MalladiGenomics inventoryhttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/13Copath All table2019-07-09T14:34:30-05:00Venkat MalladiCopath All tablehttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/12CopathMets table2019-07-09T14:34:21-05:00Venkat MalladiCopathMets tablehttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/10Diagnosis TR table2019-07-09T14:34:04-05:00Venkat MalladiDiagnosis TR tablehttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/7IHC2019-07-09T14:33:38-05:00Venkat MalladiIHChttps://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 Barnes