ngs_tools issueshttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues2019-02-12T10:40:41Zhttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/33ms_workflow: report settings from MaxQuant log file2019-02-12T10:40:41Zhersemanms_workflow: report settings from MaxQuant log filehersemanhersemanhttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/30ms_workflow: add option to run analysis on raw intensities instead of LFQs2019-01-15T15:17:59Zhersemanms_workflow: add option to run analysis on raw intensities instead of LFQshersemanhersemanhttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/29revise limma workflow for mass spec data2019-01-11T15:10:10Zhersemanrevise limma workflow for mass spec data- start new script in ms_workflow folder- start new script in ms_workflow folderhersemanhersemanhttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/28ms_workflow: Improvemnts2019-12-10T08:25:51Zbrandlbrandl@mpi-cbg.dems_workflow: Improvemnts- [x] separate protein groups
- [x] report 0-proportions similar to NAs
- [x] expose renaming scheme as an argument
- [ ] `protein_acc` extraction depends on study (with/witnout name, w/o separator). Need to generify `protein_acc=str_spl...- [x] separate protein groups
- [x] report 0-proportions similar to NAs
- [x] expose renaming scheme as an argument
- [ ] `protein_acc` extraction depends on study (with/witnout name, w/o separator). Need to generify `protein_acc=str_split_fixed(protein_ids, "[|]", 3)`. One way: `--extract extrac_acc.R` which defines extractor function -> `protein_acc=extract_fun(protein_ids)`
- [x] detect presence/absence of identifcation types --> conditionaed executino of corresponding bits
- [ ] try to postpone annotation handling to end of data-prep workflow/analysis
- [x] fix result table links _#' [identSummary](`r add_prefix("ident_types_summary.txt")`)_
- [x] How to auto-adjust imputation proportion?
- [x] We just need imputation because we want an abundance matrix for limma. for t-tests neither na->0 nor impuations are required because we can work with long data.
limma
* also show batch-corrected qc plots (clustering, pca)
* _man muss das mal alles durchschauen_
* why does the voom with a `~condition` design fix the sample clustering in `file:///Volumes/project-stepien/stepien_ms_fractions/data/limma/p_vs_s/dge_limma.html`
* add condition/sample colors to _voom vs raw_ plot
* externalize annotation of results
* why do ma plots look so weired?
![image](/uploads/bcf9f12174dc8d16f35795496ce46856/image.png)hersemanhersemanhttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/27new ticket2018-12-07T15:14:31Zbrandlbrandl@mpi-cbg.denew ticket@herseman
this needs to be fixed asap@herseman
this needs to be fixed asaphttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/26update to more recent https://github.com/deeptools/deepTools/releases2020-02-20T14:19:37Zbrandlbrandl@mpi-cbg.deupdate to more recent https://github.com/deeptools/deepTools/releaseshttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/25report improvements2020-02-20T14:19:05Zbrandlbrandl@mpi-cbg.dereport improvements* remove pointless R output **[done]**
* include materials and methods section
* explain algn efficiency
* more docu for lib-complexity in fastqc report
* add Figure 9.3: Features: genes seen in the whole data set. The x-axis displays t...* remove pointless R output **[done]**
* include materials and methods section
* explain algn efficiency
* more docu for lib-complexity in fastqc report
* add Figure 9.3: Features: genes seen in the whole data set. The x-axis displays the number of uniquely aligned fragments and the y-axis shows how many features are seen within each x subset of fragments.
* add PCA (1−2) of top 500 most diverse genes
* add toc (floating if we can adjust content width) or via markdown if not **[done]**
* detail out column model of main results table(s)
* render ensbml link in interactive table (make sure to also include non-ensembl data)
* prep example data for testing
* use symbols for "Extract most signifiantly changed genes and display" heatmap (if present)https://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/23consider to use alpha for more correct p_adjustment2020-05-14T10:46:43Zbrandlbrandl@mpi-cbg.deconsider to use alpha for more correct p_adjustmentsequencing facility is using it!
alpha
the significance cutoff used for optimizing the independent filtering (by default 0.1). If the adjusted p-value cutoff (FDR) will be a value other than 0.1, alpha should be set to that value.
See ...sequencing facility is using it!
alpha
the significance cutoff used for optimizing the independent filtering (by default 0.1). If the adjusted p-value cutoff (FDR) will be a value other than 0.1, alpha should be set to that value.
See https://github.com/mlesche/dsp/blob/master/dsp/r_scripts/deseq_report.r#L410hersemanhersemanhttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/22write shiny app (results relative local app) for dge data2018-01-19T08:42:03Zhersemanwrite shiny app (results relative local app) for dge dataaim: explore normalized count data of diffex data
- plot normalized counts for each replicate per condition
- provide table with contrast details (dge data: logfc etc.)
impl better means to access summary and quality statististcs
learn ...aim: explore normalized count data of diffex data
- plot normalized counts for each replicate per condition
- provide table with contrast details (dge data: logfc etc.)
impl better means to access summary and quality statististcs
learn from https://sourceforge.net/projects/quickrnaseq example report https://github.com/baohongz/QuickRNASeq
further options:
- provide a condition rearranger to manipulate the plot
- include kallisto and STAR expression profileshttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/19use common q-score color scale for enrichment plots in cp_enrichment.R2017-11-09T17:54:56Zbrandlbrandl@mpi-cbg.deuse common q-score color scale for enrichment plots in cp_enrichment.Rhttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/18impl better means to access summary and quality statististcs2017-11-09T15:37:41Zbrandlbrandl@mpi-cbg.deimpl better means to access summary and quality statististcslearn from https://sourceforge.net/projects/quickrnaseq
example report https://github.com/baohongz/QuickRNASeqlearn from https://sourceforge.net/projects/quickrnaseq
example report https://github.com/baohongz/QuickRNASeqhttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/17better handling of outliers2019-03-07T15:19:51Zbrandlbrandl@mpi-cbg.debetter handling of outliersallow to differentiate between outliers and non-expressed genesallow to differentiate between outliers and non-expressed geneshttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/16auto-detect strandedness when extracting count matrix2020-03-27T14:32:23Zbrandlbrandl@mpi-cbg.deauto-detect strandedness when extracting count matrixsee dge_workflow/dge_utils.sh:357see dge_workflow/dge_utils.sh:357https://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/15try RNA-SeQC to get qc for bam files2019-12-09T13:42:04Zbrandlbrandl@mpi-cbg.detry RNA-SeQC to get qc for bam fileshttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/14export TPM instead of FPKM tables2017-06-19T11:19:42Zbrandlbrandl@mpi-cbg.deexport TPM instead of FPKM tableshersemanhersemanhttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/13Change bam_qc to report multi/single mapper proportions relative to number of...2019-03-07T15:19:04Zbrandlbrandl@mpi-cbg.deChange bam_qc to report multi/single mapper proportions relative to number of aligned reads.https://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/12Add option to perform diffex-test in mf_feat_counts.R using fc-cutoff > 0.2017-06-19T07:58:38Zbrandlbrandl@mpi-cbg.deAdd option to perform diffex-test in mf_feat_counts.R using fc-cutoff > 0.brandlbrandl@mpi-cbg.debrandlbrandl@mpi-cbg.dehttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/11Integrate tools to assess gc/3/5 bias, insert size, and capture efficiency2020-02-20T12:42:13Zbrandlbrandl@mpi-cbg.deIntegrate tools to assess gc/3/5 bias, insert size, and capture efficiencye.g. using http://deeptools.readthedocs.io/en/latest/content/tools/computeGCBias.html?highlight=bias
(see "Multi-perspective quality control of Illumina RNA sequencing data analysis" http://bfg.oxfordjournals.org/content/early/2016/09/28...e.g. using http://deeptools.readthedocs.io/en/latest/content/tools/computeGCBias.html?highlight=bias
(see "Multi-perspective quality control of Illumina RNA sequencing data analysis" http://bfg.oxfordjournals.org/content/early/2016/09/28/bfgp.elw035.abstract )
@lakshman opinion?https://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/10use http://multiqc.info/ for qc reporting2019-11-18T09:06:51Zbrandlbrandl@mpi-cbg.deuse http://multiqc.info/ for qc reportinghttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/9Export counts as TPM in featcounts_deseq_mf.R2017-07-08T23:44:42Zbrandlbrandl@mpi-cbg.deExport counts as TPM in featcounts_deseq_mf.RThey are better than fpkm according to Mathias and allow for better comparison across samplesThey are better than fpkm according to Mathias and allow for better comparison across samplesbrandlbrandl@mpi-cbg.debrandlbrandl@mpi-cbg.de