From 7c189dececed995a7c215615104e9661511b6da2 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 20 Aug 2024 18:55:48 +0200 Subject: [PATCH 1/6] Animate subway map --- docs/images/nf-core-rnaseq_metro_map_grey.svg | 5650 +++++++++-------- 1 file changed, 2893 insertions(+), 2757 deletions(-) diff --git a/docs/images/nf-core-rnaseq_metro_map_grey.svg b/docs/images/nf-core-rnaseq_metro_map_grey.svg index 7b55ae7e5..c49117c96 100644 --- a/docs/images/nf-core-rnaseq_metro_map_grey.svg +++ b/docs/images/nf-core-rnaseq_metro_map_grey.svg @@ -2782,9 +2782,9 @@ borderopacity="1.0" inkscape:pageopacity="0.0" inkscape:pageshadow="2" - inkscape:zoom="0.57000002" - inkscape:cx="1418.421" - inkscape:cy="572.807" + inkscape:zoom="0.40305088" + inkscape:cx="851.00918" + inkscape:cy="857.21188" inkscape:document-units="mm" inkscape:current-layer="layer1" showgrid="false" @@ -2823,2796 +2823,2932 @@ inkscape:groupmode="layer" id="layer1" transform="translate(64.401787,107.17563)">1catfastqSTAGE2. Genome alignment & quantification3. Pseudo-alignment & quantification1. Pre-processing4. Post-processing3SalmonKallistoMultiQCTSV5RSeQC(multiple modules)Preseq4SAMtools(sort, index, stats)BEDtoolsgenomecovbedGraphToBigWig GermlineSarek BIGWIGHTMLHTML ExomedupRadar GermlineSarek BAMBAI ExomeTSV GermlineSarek 1catfastqSTAGE2. Genome alignment & quantification3. Pseudo-alignment & quantification1. Pre-processing4. Post-processing3SalmonKallistoMultiQC5RSeQC(multiple modules)Preseq4SAMtools(sort, index, stats)BEDtoolsgenomecovbedGraphToBigWigStringTiepicardMarkDuplicatesdupRadarMultiQCPseudo-aligner: Salmon, Quantification: SalmonAligner: HISAT2, Quantification: NoneQualimaprnaseqDESeq2(PCA only) + id="tspan145" + x="169.25996" + y="120.60331" + style="font-style:normal;font-variant:normal;font-weight:bold;font-stretch:normal;font-size:5.64444px;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro Bold';text-align:start;text-anchor:start;fill:#000000;stroke:none;stroke-width:0.264583;stroke-opacity:1">Aligner: STAR, Quantification: Salmon (default)Pseudo-aligner: Kallisto, Quantification: KallistoAligner: STAR, Quantification: RSEMMETHODLicense:STAGE2. Genome alignment & quantification3. Pseudo-alignment & quantification5. Final QC1. Pre-processing4. Post-processingcatfastqTrimGalore!SortMeRNAFastQCinferstrandedness(fq, Salmon)BBSplitUMI-toolsextractFastQCFastP12STARSalmonHISAT2RSEMUMI-toolsdedupQualimaprnaseqDESeq2(PCA only) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From 1087b2622d252e81af56433762e5eacd3c7bed39 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 21 Aug 2024 19:53:13 +0200 Subject: [PATCH 2/6] animate metro map --- README.md | 2 +- docs/images/nf-core-rnaseq_metro_map_grey.svg | 5650 ++++++++-------- ...nf-core-rnaseq_metro_map_grey_animated.svg | 5754 +++++++++++++++++ 3 files changed, 8512 insertions(+), 2894 deletions(-) create mode 100644 docs/images/nf-core-rnaseq_metro_map_grey_animated.svg diff --git a/README.md b/README.md index 411dfd3f4..2c1e9f0dc 100644 --- a/README.md +++ b/README.md @@ -20,7 +20,7 @@ **nf-core/rnaseq** is a bioinformatics pipeline that can be used to analyse RNA sequencing data obtained from organisms with a reference genome and annotation. It takes a samplesheet and FASTQ files as input, performs quality control (QC), trimming and (pseudo-)alignment, and produces a gene expression matrix and extensive QC report. -![nf-core/rnaseq metro map](docs/images/nf-core-rnaseq_metro_map_grey.png) +![nf-core/rnaseq metro map](docs/images/nf-core-rnaseq_metro_map_grey_animated.svg) 1. Merge re-sequenced FastQ files ([`cat`](http://www.linfo.org/cat.html)) 2. Auto-infer strandedness by subsampling and pseudoalignment ([`fq`](https://github.com/stjude-rust-labs/fq), [`Salmon`](https://combine-lab.github.io/salmon/)) diff --git a/docs/images/nf-core-rnaseq_metro_map_grey.svg b/docs/images/nf-core-rnaseq_metro_map_grey.svg index c49117c96..7b55ae7e5 100644 --- a/docs/images/nf-core-rnaseq_metro_map_grey.svg +++ b/docs/images/nf-core-rnaseq_metro_map_grey.svg @@ -2782,9 +2782,9 @@ borderopacity="1.0" inkscape:pageopacity="0.0" inkscape:pageshadow="2" - inkscape:zoom="0.40305088" - inkscape:cx="851.00918" - inkscape:cy="857.21188" + inkscape:zoom="0.57000002" + inkscape:cx="1418.421" + inkscape:cy="572.807" inkscape:document-units="mm" inkscape:current-layer="layer1" showgrid="false" @@ -2823,2932 +2823,2796 @@ inkscape:groupmode="layer" id="layer1" transform="translate(64.401787,107.17563)">