BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2021-07-19T13:42:12-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/30non-biological reads needs renaming2021-07-19T13:42:12-05:00Venkat Malladinon-biological reads needs renamingRejected reads are downloaded but not named appropriatley.Rejected reads are downloaded but not named appropriatley.https://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/29Paired-end2021-07-19T13:41:28-05:00Venkat MalladiPaired-endPaired-end is not used anywere in the pipelinesPaired-end is not used anywere in the pipelineshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/52Generate QC Plot2020-09-18T12:33:29-05:00Jeremy MathewsGenerate QC PlotIn preparation for a Seurat analysis workflow, the addition of a Violin Plot to display QC for count results can be used to determine inputs for Seurat workflow.
@ghenry has an automated script to determine optimal cutoff values for fil...In preparation for a Seurat analysis workflow, the addition of a Violin Plot to display QC for count results can be used to determine inputs for Seurat workflow.
@ghenry has an automated script to determine optimal cutoff values for filtering data. Use the violin plot code below and overlay it with markers of cutoff values.
If values are acceptable, then use "automatic" option in Seurat workflow, else use "manual" and select the cutoffs for filtering data by hand.
"""
VlnPlot(object, features = c("nFeature_RNA", "nCount_RNA", "percent.mt"), ncol = 3)
"""https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/42Update to Astocyte 0.4.02020-09-07T06:43:20-05:00Venkat MalladiUpdate to Astocyte 0.4.0# Summary
New Astrocyte 0.4.0 features to test
* [x] Customized configuration file in yaml
* [x] Load specific singularity version
* [x] Load Nextflow version
* [x] Add citation in yaml file
/cc @ghenry @venkat.malladi @s18170...# Summary
New Astrocyte 0.4.0 features to test
* [x] Customized configuration file in yaml
* [x] Load specific singularity version
* [x] Load Nextflow version
* [x] Add citation in yaml file
/cc @ghenry @venkat.malladi @s181706 @s189701Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/27Add flag for SAM instead of FastQ2020-08-26T11:06:35-05:00Jonathan GesellAdd flag for SAM instead of FastQCreate an option if users want to download the SAM file instead of the FastQ files.Create an option if users want to download the SAM file instead of the FastQ files.Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/26Fix issue downloading and spliting for single cell data2020-08-21T14:20:59-05:00Venkat MalladiFix issue downloading and spliting for single cell dataThere is an issue of properly splitting single-cell data if I, R1, R2 reads are all uploadedThere is an issue of properly splitting single-cell data if I, R1, R2 reads are all uploadedhttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/88create down-sampled test data2020-08-07T10:17:20-05:00Spencer Barnescreate down-sampled test dataCreate down-sampled fastq's for quick tests when applying bug fixes.Create down-sampled fastq's for quick tests when applying bug fixes.Spencer BarnesSpencer Barneshttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/20Pipeline maintaince documentation2021-04-06T08:15:08-05:00Venkat MalladiPipeline maintaince documentationhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/41Add test for astrocyte specific run of pipline2020-10-30T11:48:42-05:00Venkat MalladiAdd test for astrocyte specific run of pipline# Summary
* [x] Add test for astrocyte-specific test besides cli
* [x] Add Badge for astrocyte
* [x] Test for astrocyte 0.4.0 instead of loading astrocyte
/cc @ghenry @venkat.malladi @s181706 @s189701# Summary
* [x] Add test for astrocyte-specific test besides cli
* [x] Add Badge for astrocyte
* [x] Test for astrocyte 0.4.0 instead of loading astrocyte
/cc @ghenry @venkat.malladi @s181706 @s189701https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/49Add test for astrocyte 0.3.12020-08-02T09:57:17-05:00Venkat MalladiAdd test for astrocyte 0.3.1# Summary
* [ ] Add test for astrocyte-specific test besides cli
* [ ] Add Badge for astrocyte
* [ ] Test for astrocyte 0.3.1 instead of loading astrocyte
/cc @ghenry# Summary
* [ ] Add test for astrocyte-specific test besides cli
* [ ] Add Badge for astrocyte
* [ ] Test for astrocyte 0.3.1 instead of loading astrocyte
/cc @ghenryGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/25update test for astrocyte 0.3.12020-06-26T15:38:59-05:00Venkat Malladiupdate test for astrocyte 0.3.1Add test for astrocyte
update Readme to have astrocyte badgeAdd test for astrocyte
update Readme to have astrocyte badgehttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/22Parallelize tests2020-06-16T09:35:08-05:00Jonathan GesellParallelize testsRe-write the tests using a combination of joblib.Parallel and pytest-parallel to see if we can speed up the tests. Note: on Nucleus009, we want to keep the core usage count down to no more than 4 cores.Re-write the tests using a combination of joblib.Parallel and pytest-parallel to see if we can speed up the tests. Note: on Nucleus009, we want to keep the core usage count down to no more than 4 cores.Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/28Comparison Script2020-04-25T19:02:01-05:00Venkat MalladiComparison ScriptComparison between current database and updates.Comparison between current database and updates.Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/27New Beaker code2020-04-25T18:55:13-05:00Venkat MalladiNew Beaker codeVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/13nullDataError2020-04-20T10:55:45-05:00Jonathan GesellnullDataErrorNeeds to throw an error when srapath returns null, example:
SRS070511Needs to throw an error when srapath returns null, example:
SRS070511Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/26Add tests surgery2020-02-07T09:26:16-06:00Venkat MalladiAdd tests surgeryhttps://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/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 Mathews