Merge pull request #71 from GoekeLab/update_readme

fix update in genome browser link format
GoekeLab · Nov 28, 2024 · 1ea548a · 1ea548a
2 parents 340ed4b + c823ee3
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diff --git a/README.md b/README.md
@@ -33,7 +33,7 @@ https://groups.google.com/forum/#!forum/sg-nex-updates/join
 
 ## Data Release and Access
 
-**Latest Release (v0.5)**
+**Latest Release (v0.6)**
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10795697.svg)](https://doi.org/10.5281/zenodo.10795697)
 
@@ -68,6 +68,14 @@ Chen, Y. _et al._ "A systematic benchmark of Nanopore long read RNA sequencing f
 
 **Release Note & Updates**
 
+Version Number: V0.6.0                
+Date: 2024-11-21               
+Replacement of fastq and bam files                              
+- fastq files basecalled from fast5 converted blow5 files using Guppy 6.4.2 
+- bam files using updated fastq files with Minimap2-2.22 
+
+Added in code for SG-NEx manuscript 
+
 Version Number: V0.5.1       
 Date: 2024-04-15
 Release of new sample     
@@ -106,7 +114,7 @@ You can find previous releases here in the [release history](https://github.com/
 
 You can now browse the data using the UCSC genome browser:
 
-[View the SG-NEx data in the UCSC Genome Browser](http://genome.ucsc.edu/cgi-bin/hgTracks?db=grch38&hubUrl=https://sg-nex-data.s3.amazonaws.com/data/sequencing_data_ont/genome_browser_data/hub_track/hub-ONT-Grch38-complete-2024-01-19.txt)
+[View the SG-NEx data in the UCSC Genome Browser](http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hubUrl=https://sg-nex-data.s3.amazonaws.com/data/sequencing_data_ont/genome_browser_data/hub_track/hub-ONT-Grch38-complete-2024-01-19.txt)
 
 By default only selected tracks are shown, but you can visualise all reads (bigbed tracks) and their coverage tracks (bigwig) from each individual sample.
 

diff --git a/docs/samples.tsv b/docs/samples.tsv
@@ -1,4 +1,4 @@
-sample_alias	Spike in concentration	cellLine	protocol	flowcell	kit	Platform	Mux_id	basecaller_version*	generation_date	matched_RNA_modification_data	fast5_path	fastq_path	genome_bam_path	transcriptome_bam_path	bigbed_path	bigwig_path	fast5_ENA[not recommended for download]	fastq_ENA[not recommended for download]	blow5_path	blow5_index_path
+sample_alias	Spike in concentration	cellLine	protocol	flowcell	kit	Platform	Mux_id	basecaller_version(ENA)*	generation_date	matched_RNA_modification_data	fast5_path	fastq_path	genome_bam_path	transcriptome_bam_path	bigbed_path	bigwig_path	fast5_ENA[not recommended for download]	fastq_ENA[not recommended for download]	blow5_path	blow5_index_path
 SGNex_A549_cDNA_replicate1_run2		A549	cDNA	FLO-MIN106	SQK-PCS108	MinION		albacore-GIS	20180629		https://sg-nex-data.s3.ap-southeast-1.amazonaws.com/data/sequencing_data_ont/fast5/SGNex_A549_cDNA_replicate1_run2/SGNex_A549_cDNA_replicate1_run2.tar.gz	https://sg-nex-data.s3.ap-southeast-1.amazonaws.com/data/sequencing_data_ont/fastq/SGNex_A549_cDNA_replicate1_run2/SGNex_A549_cDNA_replicate1_run2.fastq.gz	https://sg-nex-data.s3.ap-southeast-1.amazonaws.com/data/sequencing_data_ont/bam/genome/SGNex_A549_cDNA_replicate1_run2/SGNex_A549_cDNA_replicate1_run2.bam	https://sg-nex-data.s3.ap-southeast-1.amazonaws.com/data/sequencing_data_ont/bam/transcriptome/SGNex_A549_cDNA_replicate1_run2/SGNex_A549_cDNA_replicate1_run2.bam	https://sg-nex-data.s3.ap-southeast-1.amazonaws.com/data/sequencing_data_ont/genome_browser_data/bigbed/SGNex_A549_cDNA_replicate1_run2.bigbed	https://sg-nex-data.s3.ap-southeast-1.amazonaws.com/data/sequencing_data_ont/genome_browser_data/bigwig/SGNex_A549_cDNA_replicate1_run2.bigwig	ftp.sra.ebi.ac.uk/vol1/run/ERR928/ERR9286391/SGNex_A549_cDNA_replicate1_run2.tar.gz	ftp.sra.ebi.ac.uk/vol1/fastq/ERR605/006/ERR6053016/ERR6053016.fastq.gz	https://sg-nex-data-blow5.s3.ap-southeast-1.amazonaws.com/SGNex_A549_cDNA_replicate1_run2/SGNex_A549_cDNA_replicate1_run2.blow5	https://sg-nex-data-blow5.s3.ap-southeast-1.amazonaws.com/SGNex_A549_cDNA_replicate1_run2/SGNex_A549_cDNA_replicate1_run2.blow5.idx
 SGNex_A549_cDNAStranded_replicate3_run3		A549	cDNAStranded	FLO-MIN106	SQK-PCS109	MinION		albacore-GIS	20181030		https://sg-nex-data.s3.ap-southeast-1.amazonaws.com/data/sequencing_data_ont/fast5/SGNex_A549_cDNAStranded_replicate3_run3/SGNex_A549_cDNAStranded_replicate3_run3.tar.gz	https://sg-nex-data.s3.ap-southeast-1.amazonaws.com/data/sequencing_data_ont/fastq/SGNex_A549_cDNAStranded_replicate3_run3/SGNex_A549_cDNAStranded_replicate3_run3.fastq.gz	https://sg-nex-data.s3.ap-southeast-1.amazonaws.com/data/sequencing_data_ont/bam/genome/SGNex_A549_cDNAStranded_replicate3_run3/SGNex_A549_cDNAStranded_replicate3_run3.bam	https://sg-nex-data.s3.ap-southeast-1.amazonaws.com/data/sequencing_data_ont/bam/transcriptome/SGNex_A549_cDNAStranded_replicate3_run3/SGNex_A549_cDNAStranded_replicate3_run3.bam	https://sg-nex-data.s3.ap-southeast-1.amazonaws.com/data/sequencing_data_ont/genome_browser_data/bigbed/SGNex_A549_cDNAStranded_replicate3_run3.bigbed	https://sg-nex-data.s3.ap-southeast-1.amazonaws.com/data/sequencing_data_ont/genome_browser_data/bigwig/SGNex_A549_cDNAStranded_replicate3_run3.bigwig	ftp.sra.ebi.ac.uk/vol1/run/ERR928/ERR9286392/SGNex_A549_cDNAStranded_replicate3_run3.tar.gz	ftp.sra.ebi.ac.uk/vol1/fastq/ERR605/007/ERR6053017/ERR6053017.fastq.gz	https://sg-nex-data-blow5.s3.ap-southeast-1.amazonaws.com/SGNex_A549_cDNAStranded_replicate3_run3/SGNex_A549_cDNAStranded_replicate3_run3.blow5	https://sg-nex-data-blow5.s3.ap-southeast-1.amazonaws.com/SGNex_A549_cDNAStranded_replicate3_run3/SGNex_A549_cDNAStranded_replicate3_run3.blow5.idx
 SGNex_A549_cDNAStranded_replicate5_run2		A549	cDNAStranded	FLO-MIN106D	SQK-PCS109	MinION		guppy-2.1.3-albacore	20181217		https://sg-nex-data.s3.ap-southeast-1.amazonaws.com/data/sequencing_data_ont/fast5/SGNex_A549_cDNAStranded_replicate5_run2/SGNex_A549_cDNAStranded_replicate5_run2.tar.gz	https://sg-nex-data.s3.ap-southeast-1.amazonaws.com/data/sequencing_data_ont/fastq/SGNex_A549_cDNAStranded_replicate5_run2/SGNex_A549_cDNAStranded_replicate5_run2.fastq.gz	https://sg-nex-data.s3.ap-southeast-1.amazonaws.com/data/sequencing_data_ont/bam/genome/SGNex_A549_cDNAStranded_replicate5_run2/SGNex_A549_cDNAStranded_replicate5_run2.bam	https://sg-nex-data.s3.ap-southeast-1.amazonaws.com/data/sequencing_data_ont/bam/transcriptome/SGNex_A549_cDNAStranded_replicate5_run2/SGNex_A549_cDNAStranded_replicate5_run2.bam	https://sg-nex-data.s3.ap-southeast-1.amazonaws.com/data/sequencing_data_ont/genome_browser_data/bigbed/SGNex_A549_cDNAStranded_replicate5_run2.bigbed	https://sg-nex-data.s3.ap-southeast-1.amazonaws.com/data/sequencing_data_ont/genome_browser_data/bigwig/SGNex_A549_cDNAStranded_replicate5_run2.bigwig	ftp.sra.ebi.ac.uk/vol1/run/ERR928/ERR9286467/SGNex_A549_cDNAStranded_replicate5_run2.tar.gz	ftp.sra.ebi.ac.uk/vol1/fastq/ERR605/008/ERR6053018/ERR6053018.fastq.gz	https://sg-nex-data-blow5.s3.ap-southeast-1.amazonaws.com/SGNex_A549_cDNAStranded_replicate5_run2/SGNex_A549_cDNAStranded_replicate5_run2.blow5	https://sg-nex-data-blow5.s3.ap-southeast-1.amazonaws.com/SGNex_A549_cDNAStranded_replicate5_run2/SGNex_A549_cDNAStranded_replicate5_run2.blow5.idx

diff --git a/images/folder_index.png b/images/folder_index.png