home.md

@@ -49,3 +49,29 @@
 | 2019 | Shiny-Seq - https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-019-4471-1 |
 | | https://github.com/nf-core/rnaseq |
 | | NGS-pipe - https://github.com/cbg-ethz/NGS-pipe/wiki |
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+## Metrics for comparing pipelines for RNA-seq analysis
+* Input 
+  * size of the input that needs to be provided
+  * type: Accessions - repositories / Fastq files
+  * automated inferences: type of sample preparation, adaptors
+* Output
+  * sample quality metrics
+    * complexity
+    * mapping rate
+    * duplication level
+    * saturation level
+    * RNA integrity
+  * bam files
+  * quantification
+    * gene level
+    * isoform level
+    * annotation categories
+    * proportion structural RNAs
+    * includes multi-mappers
+  * inference
+    * novel isoforms: splicing/polyadenylation
+    * SNPs/mutations
+* Number/type of supported platforms
+* Desktop application/needs cluster