Add skera examples (#10)

Co-authored-by: Jessica Mattick <jmattick@pacificbiosciences.com>

docs/adapters.md

@@ -18,6 +18,8 @@ order of adapters in the reads. There should be one entry per adapter (forward
 or reverse-complement orientation) with no overlapping adapter sequences. 
 Duplicate names or sequences are not allowed.
 
+An example MAS adapter fasta can be downloaded [here](https://downloads.pacbcloud.com/public/dataset/MAS-Seq/REF-MAS_adapters/MAS-Seq_Adapter_v1/).
+
 ```
 >A
 AGCTTACTTGTGAAGA

docs/examples.md

@@ -0,0 +1,23 @@
+---
+layout: default
+title: Examples
+nav_order: 4
+description: "Skera examples"
+---
+
+## CLI example
+
+Data generated using the [MAS-Seq for single-cell IsoSeq kit](https://www.pacb.com/products-and-services/applications/rna-sequencing/single-cell-rna-sequencing/) on either Sequel IIe or Revio can be downloaded [here](https://downloads.pacbcloud.com/public/dataset/MAS-Seq/).
+
+```
+# download HiFi reads for MAS-Seq PBMCs run on Sequel IIe
+wget https://downloads.pacbcloud.com/public/dataset/MAS-Seq/DATA-SQ2-PBMC_5kcells/0-CCS/m64476e_220618_014917.hifi_reads.bam
+
+# download MAS adapter fasta
+wget https://downloads.pacbcloud.com/public/dataset/MAS-Seq/REF-MAS_adapters/MAS-Seq_Adapter_v1/mas16_primers.fasta
+
+# run skera split to generate segmented reads
+skera split m64476e_220618_014917.hifi_reads.bam mas16_primers.fasta segmented.bam
+```
+
+An example of the `segmented.bam` output can be found [here](https://downloads.pacbcloud.com/public/dataset/MAS-Seq/DATA-SQ2-PBMC_5kcells/1-Sreads/)

docs/index.md

@@ -10,14 +10,16 @@ permalink: /
   <img src="img/skera-header.png" alt="skera logo" width="600px"/>
 </p>
 
-_Skera_ splits arrayed PacBio HiFi reads at adapter positions generating segmented reads 
+
+
+_Skera_ splits [MAS-Seq](https://www.pacb.com/products-and-services/applications/rna-sequencing/single-cell-rna-sequencing/) PacBio HiFi reads at adapter positions generating segmented reads 
 ([S-reads](/read-segments)). For each input/parent read (e.g. HiFi)
 _skera_ will create multiple bam records, one for each S-read. A parent read
 can contain many S-reads. _Skera_ has two major functions, split and undo.
 _Skera_ undo reconstitutes the original parent read from input S-reads.
 
 ## Availability
-The latest `skera` can be installed via the bioconda.
+The latest version can be installed via bioconda package `pbskera`.
 
 Please refer to our [official pbbioconda
 page](https://github.com/PacificBiosciences/pbbioconda) for information on
@@ -27,7 +29,7 @@ Installation, Support, License, Copyright, and Disclaimer.
 Version **0.1.0**: [Full changelog here](/changelog)
 
 ## Input
-### Reads
+### HiFi Reads
 HiFi reads in PacBio BAM format.
 
 ### Adapters

docs/output.md

@@ -0,0 +1,32 @@
+---
+layout: default
+title: Output Files
+nav_order: 4
+description: "Skera Output Files"
+---
+
+## Output Files
+
+### Segmented BAM files
+
+* `segmented.bam`
+
+  _Skera_ outputs a BAM file containing all [segmented reads](/read-segments) that have sequential leading and trailing adapters based on the order of [adapters](/adapters) in the input fasta. 
+
+* `segmented.non_passing.bam`
+
+  The `non_passing.bam` file contains the bam records that have adapters found in non-sequential order. This file is necessary for `skera undo`. 
+
+### Reports
+
+* `summary.csv`
+
+  The `summary.csv` contains general summary statistics for read segmentation. 
+
+* `ligations.csv`
+
+  The `ligations.csv` file contains the counts of all leading and trailing adapter combinations found in all passing and non-passing segments.
+
+* `read_lengths.csv`
+
+    The `read_lengths.csv` file contains the parent HiFi and s-read lengths for all passing segments.