From 763c6e5d0864160a9d8bac2fde175f00d0836fdf Mon Sep 17 00:00:00 2001 From: igor Date: Wed, 24 May 2017 11:41:27 -0400 Subject: [PATCH] add route description links --- README.md | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index 26b7130..6ea6c21 100644 --- a/README.md +++ b/README.md @@ -56,22 +56,22 @@ Routes are different analysis workflows. Generic routes are sample-centric (same analysis is performed for each sample). Available routes: -* `rna-star`: RNA-seq using STAR. Generates BAMs, normalized bigWigs, counts matrix, and various QC metrics. -* `rna-rsem`: RNA-seq using RSEM. Generates FPKM/TPM/counts matrix and various QC metrics. -* `rna-snv`: RNA-seq variant detection. Generates BAMs, VCFs, and various QC metrics. -* `wgbs`: WGBS using Bismark. -* `rrbs`: RRBS using Bismark. -* `wes`: Whole genome/exome/targeted variant detection. Generates BAMs, VCFs, and various QC metrics. -* `atac`: ATAC-seq. Generates BAMs, bigWigs, peaks, nucleosome positions, and various QC metrics. -* `species`: Species/metagenomics/contamination analysis. +* [rna-star](https://github.com/igordot/sns/blob/master/routes/rna-star.md): RNA-seq using STAR. Generates BAMs, normalized bigWigs, counts matrix, and various QC metrics. +* [rna-rsem](https://github.com/igordot/sns/blob/master/routes/rna-rsem.md): RNA-seq using RSEM. Generates FPKM/TPM/counts matrix and various QC metrics. +* [rna-snv](https://github.com/igordot/sns/blob/master/routes/rna-snv.md): RNA-seq variant detection. Generates BAMs, VCFs, and various QC metrics. +* [wgbs](https://github.com/igordot/sns/blob/master/routes/rrbs.md): WGBS methylation analysis. +* [rrbs](https://github.com/igordot/sns/blob/master/routes/rrbs.md): RRBS methylation analysis. +* [wes](https://github.com/igordot/sns/blob/master/routes/wes.md): Whole genome/exome/targeted variant detection. Generates BAMs, VCFs, and various QC metrics. +* [atac](https://github.com/igordot/sns/blob/master/routes/atac.md): ATAC-seq. Generates BAMs, bigWigs, peaks, nucleosome positions, and various QC metrics. +* [species](https://github.com/igordot/sns/blob/master/routes/species.md): Species/metagenomics/contamination analysis. There are additional routes for comparing groups of samples after individual samples are processed with a generic route. They depend on the output of the generic routes and must be run from the same directory. Before running, manually add proper group names or pairs to the `samples.groups.csv` or `samples.pairs.csv` files (depending on the comparison type). Available comparison routes: -* `rna-star-groups-dge`: Differential gene expression using DESeq2 for the `rna-star` results. -* `wes-pairs-snv`: Somatic variant detection for the `wes` results. +* [rna-star-groups-dge](https://github.com/igordot/sns/blob/master/routes/rna-star-groups-dge.md): Differential gene expression using DESeq2 for the `rna-star` results. +* [wes-pairs-snv](https://github.com/igordot/sns/blob/master/routes/wes-pairs-snv.md): Somatic variant detection for the `wes` results. ## Output @@ -79,6 +79,8 @@ Available comparison routes: * `summary-combined.*.csv`: Combined segment summaries table that provides a comprehensive overview of the project. * `logs-*` directories: Most stdout/stderr output will be placed here. The information can be used for tracking progress and troubleshooting. +Each route has a description with more specific details. + ## About SNS is designed to work on NYULMC HPC cluster using the Sun Grid Engine job scheduler.