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Merge pull request #71 from GoekeLab/update_readme
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fix update in genome browser link format
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@cying111
cying111 authored Nov 28, 2024
2 parents 340ed4b + c823ee3 commit 1ea548a
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12 changes: 10 additions & 2 deletions README.md
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## 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)

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**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
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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.

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2 changes: 1 addition & 1 deletion docs/samples.tsv
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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
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