GoekeLab · cying111 · Mar 7, 2023 · Jan 14, 2023 · Feb 18, 2023 · Mar 1, 2023
diff --git a/README.md b/README.md
@@ -43,6 +43,7 @@ This release includes 86 samples from 11 different cell lines.
 You can access the following data through the [AWS Open Data Registry](https://registry.opendata.aws/sgnex/):
 
 - raw files (fast5)
+- raw files (blow5)
 - basecalled files (fastq)
 - aligned reads (genome and transcriptome) (bam)
 - tracks for visualisation (bigwig and bigbed)
@@ -89,6 +90,8 @@ The following short tutorials are available that demonstrate how to analyse the
 
 - [Identification of m6A with the SG-NEx samples (using m6Anet)](./docs/SG-NEx_m6Anet_tutorial.md)
 
+- [Basecalling and analysing SG-NEx samples in S/BLOW5 format](./docs/SG-NEx_blow5_tutorial.md)
+
 Additional, more detailed workflows can be found here:
 
 - [Transcript discovery, quantification, and differential transcript expression from long read RNA-Seq data (using Bambu)](https://github.com/GoekeLab/bambu)
@@ -108,7 +111,6 @@ Viktoriia Iakovleva, Puay Leng Lee, Lixia Xin, Hui En Vanessa Ng, Jia Min Loo, X
 
 **Statistical Modeling and Data Analytics**                     
 Ying Chen, Nadia M. Davidson, Harshil Patel, Yuk Kei Wan, Min Hao Ling, Yu Song Chuah, Naruemon Pratanwanich, Christopher Hendra, Laura Watten, Chelsea Sawyer, Dominik Stanojevic, Philip Andrew Ewels, Andreas Wilm, Mile Sikic, Alexandre Thiery, Michael I. Love, Alicia Oshlak, Jonathan Göke
-
 ## Citing the SG-NEx project
 
 The SG-NEx resource is described in:

diff --git a/docs/AWS_data_access_tutorial.md b/docs/AWS_data_access_tutorial.md
@@ -4,15 +4,18 @@ SG-NEx data source contains long read (Oxford Nanopore) RNA sequencing data for
 
 The SG-NEx S3 bucket contains the following types of data:
 
-   - [Raw sequencing signal (fast5)](#raw-sequencing-signal)            
-   - [Basecalled sequences (fastq)](#basecalled-sequences)            
-   - [Aligned sequences (bam)](#aligned-sequences)     
-   - [Data visualisation tracks (bigwig/bigbed)](#data-visualisation-tracks)        
-   - [Annotations](#annotations)            
-   - [Processed data for RNA modification detection](#processed-data)     
-   - [Sample and experiment information](#sample-and-experimental-data)               
+   - [Raw sequencing signal (fast5)](#raw-sequencing-signal)
+   - [Basecalled sequences (fastq)](#basecalled-sequences)
+   - [Aligned sequences (bam)](#aligned-sequences)
+   - [Data visualisation tracks (bigwig/bigbed)](#data-visualisation-tracks)
+   - [Annotations](#annotations)
+   - [Processed data for RNA modification detection](#processed-data)
+   - [Sample and experiment information](#sample-and-experimental-data)
 
- Below is the folder index for the open data bucket:
+The SG-NEx S3 BLOW5 bucket contains the following types of data:
+   - [Raw sequencing signal (blow5)](#raw-sequencing-signal-in-blow5-format)
+
+Below is the folder index for the open data buckets:
 
 ![folder indexing\!](/images/folder_index.png)
 
@@ -24,6 +27,14 @@ aws s3 ls --no-sign-request s3://sg-nex-data/data/sequencing_data_ont/fast5/ # l
 aws s3 sync --no-sign-request s3://sg-nex-data/data/sequencing_data_ont/fast5/sample_name .    # download fast5 files to your local directory
 ```
 
+# Raw sequencing signal in BLOW5 format
+To access raw sequencing (blow5) files:
+
+```bash
+aws s3 ls --no-sign-request s3://sg-nex-data-blow5/ # list samples 
+aws s3 sync --no-sign-request s3://sg-nex-data-blow5/sample_name .    # download blow5 file and the index to your local directory
+```
+
 # Basecalled sequences
 To access basecalled sequencing (fastq) files:
 
@@ -90,7 +101,6 @@ aws s3 sync --no-sign-request s3://sg-nex-data/data/annotations/gtf_file .  # do
 
 ## RNA modification detection
  Long read direct RNA sequencing has allows the detection of RNA modification with RNA modification tools, such as [xPore](https://github.com/GoekeLab/xpore) and [m6Anet](https://github.com/GoekeLab/m6anet). To simplify the analysis of RNA modifications using the SG-Nex datasets, you can download the processed files to use with xPore and m6Anet. 
-
  To download the processed data for differential RNA modification analysis with xPore:
  ```bash
 aws s3 ls --no-sign-request s3://sg-nex-data/data/processed_data/xpore/  # list all samples that have processed data for RNA modification detection using xPore
@@ -106,7 +116,7 @@ These files are provided for a subset of samples, please see [here](/docs/sample
 
 # Sample and experimental data 
 
-Detailed information for each sequencing sample is provided [here](/docs/samples.tsv). The data also includes multiplexed samples which share the same fast5 files. The information about the multiplexed samples can be found [here](/docs/multiplexed_samples.tsv). The files can also be accessed directly on S3:
+Detailed information for each sequencing sample is provided [here](/docs/samples.tsv). The data also includes multiplexed samples which share the same fast5/blow5 files. The information about the multiplexed samples can be found [here](/docs/multiplexed_samples.tsv). The files can also be accessed directly on S3:
 
 
  ```bash