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  1. IGB
  2. IGBF-3447

Add HEADER.md to hotpollen Quickload describing SL5 genome source, flav. data folders

        Details

        • Type: Task
        • Status: To-Do (View Workflow)
        • Priority: Major
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
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          Description

          The "hotpollen" IGB Quickload site at https://data.bioviz.org/hotpollen has several folders with data in them, but not a lot of description. We need to document this site a bit better on the site itself in preparation for submitting papers.

          For this task, add "HEADER.md" files that document:

          Make a "zip" or "tar.gz" file with the HEADER.md files organized in a way that will make it easy for the person who deploys them on-line to put them in the right places and then view them. AL is probably going to be the person to deploy it all!

          For example, Ann thinks the easiest option for her would be to create a copy of the directory tree with folders needing HEADER.md files.

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              ann.loraine Ann Loraine created issue -
              ann.loraine Ann Loraine made changes -
              Field Original Value New Value
              Epic Link IGBF-3446 [ 22548 ]
              ann.loraine Ann Loraine made changes -
              Description The "hotpollen" IGB Quickload site at https://data.bioviz.org/hotpollen has several folders with data in them, but not a lot of description. We need to document this site a bit better on the site itself in preparation for submitting papers.

              For this task, add "HEADER.md" files that document:

              * What the SL5 June 2022 genome is - use text from IGB Quickload main; update that text if needed
              * What the SL4 June genome is - use text from IGB Quickload main; update that text if needed
              * What the flavonoid RNA-Seq data folders contain               		The "hotpollen" IGB Quickload site at https://data.bioviz.org/hotpollen has several folders with data in them, but not a lot of description. We need to document this site a bit better on the site itself in preparation for submitting papers.

              For this task, add "HEADER.md" files that document:

              * What the SL5 June 2022 genome is - use text from IGB Quickload main; update that text if needed; this can go into:
              * What the SL4 June genome is - use text from IGB Quickload main; update that text if needed
              * What the flavonoid RNA-Seq data folders contain
              ann.loraine Ann Loraine made changes -
              Description The "hotpollen" IGB Quickload site at https://data.bioviz.org/hotpollen has several folders with data in them, but not a lot of description. We need to document this site a bit better on the site itself in preparation for submitting papers.

              For this task, add "HEADER.md" files that document:

              * What the SL5 June 2022 genome is - use text from IGB Quickload main; update that text if needed; this can go into:
              * What the SL4 June genome is - use text from IGB Quickload main; update that text if needed
              * What the flavonoid RNA-Seq data folders contain               		The "hotpollen" IGB Quickload site at https://data.bioviz.org/hotpollen has several folders with data in them, but not a lot of description. We need to document this site a bit better on the site itself in preparation for submitting papers.

              For this task, add "HEADER.md" files that document:

              * What the SL5 June 2022 genome is - use text from IGB Quickload main; update that text if needed; this will be for folders: https://data.bioviz.org/hotpollen/S_lycopersicum_Sep_2019/ and https://data.bioviz.org/hotpollen/S_lycopersicum_Jun_2022/. See quickload "main" for the text that's needed: https://data.bioviz.org/quickload/
              * What the SL4 June genome is - use text from IGB Quickload main; update that text if needed
              * What the flavonoid RNA-Seq data folders contain
              ann.loraine Ann Loraine made changes -
              Description The "hotpollen" IGB Quickload site at https://data.bioviz.org/hotpollen has several folders with data in them, but not a lot of description. We need to document this site a bit better on the site itself in preparation for submitting papers.

              For this task, add "HEADER.md" files that document:

              * What the SL5 June 2022 genome is - use text from IGB Quickload main; update that text if needed; this will be for folders: https://data.bioviz.org/hotpollen/S_lycopersicum_Sep_2019/ and https://data.bioviz.org/hotpollen/S_lycopersicum_Jun_2022/. See quickload "main" for the text that's needed: https://data.bioviz.org/quickload/
              * What the SL4 June genome is - use text from IGB Quickload main; update that text if needed
              * What the flavonoid RNA-Seq data folders contain               		The "hotpollen" IGB Quickload site at https://data.bioviz.org/hotpollen has several folders with data in them, but not a lot of description. We need to document this site a bit better on the site itself in preparation for submitting papers.

              For this task, add "HEADER.md" files that document:

              * What the SL5 June 2022 and SL4 Sep 2019 genomes are - use text from IGB Quickload main; update that text if needed; this will be for folders: https://data.bioviz.org/hotpollen/S_lycopersicum_Sep_2019/ and https://data.bioviz.org/hotpollen/S_lycopersicum_Jun_2022/. See quickload "main" for the text that's needed, and also the subversion repository
              * What the flavonoid RNA-Seq data folders contain

              Make a "zip" or "tar.gz" file with the HEADER.md files organized in a way that will make it easy for the person who deploys them on-line to put them in the right places and then view them. AL is probably going to be the person to deploy it all!

              For example, Ann thinks the easiest option for her would be to create a copy of the directory tree with folders needing HEADER.md files.
              ann.loraine Ann Loraine made changes -
              Description The "hotpollen" IGB Quickload site at https://data.bioviz.org/hotpollen has several folders with data in them, but not a lot of description. We need to document this site a bit better on the site itself in preparation for submitting papers.

              For this task, add "HEADER.md" files that document:

              * What the SL5 June 2022 and SL4 Sep 2019 genomes are - use text from IGB Quickload main; update that text if needed; this will be for folders: https://data.bioviz.org/hotpollen/S_lycopersicum_Sep_2019/ and https://data.bioviz.org/hotpollen/S_lycopersicum_Jun_2022/. See quickload "main" for the text that's needed, and also the subversion repository
              * What the flavonoid RNA-Seq data folders contain

              Make a "zip" or "tar.gz" file with the HEADER.md files organized in a way that will make it easy for the person who deploys them on-line to put them in the right places and then view them. AL is probably going to be the person to deploy it all!

              For example, Ann thinks the easiest option for her would be to create a copy of the directory tree with folders needing HEADER.md files.               		The "hotpollen" IGB Quickload site at https://data.bioviz.org/hotpollen has several folders with data in them, but not a lot of description. We need to document this site a bit better on the site itself in preparation for submitting papers.

              For this task, add "HEADER.md" files that document:

              * What the SL5 June 2022 and SL4 Sep 2019 genomes are - use text from IGB Quickload main; update that text if needed; this will be for folders: https://data.bioviz.org/hotpollen/S_lycopersicum_Sep_2019/ and https://data.bioviz.org/hotpollen/S_lycopersicum_Jun_2022/. See quickload "main" for the text that's needed, and also the subversion repository
              * What the flavonoid RNA-Seq data folders contain, such as: https://data.bioviz.org/hotpollen/S_lycopersicum_Jun_2022/30-605730043/ and its sister directories

              Make a "zip" or "tar.gz" file with the HEADER.md files organized in a way that will make it easy for the person who deploys them on-line to put them in the right places and then view them. AL is probably going to be the person to deploy it all!

              For example, Ann thinks the easiest option for her would be to create a copy of the directory tree with folders needing HEADER.md files.
              ann.loraine Ann Loraine made changes -
              Description The "hotpollen" IGB Quickload site at https://data.bioviz.org/hotpollen has several folders with data in them, but not a lot of description. We need to document this site a bit better on the site itself in preparation for submitting papers.

              For this task, add "HEADER.md" files that document:

              * What the SL5 June 2022 and SL4 Sep 2019 genomes are - use text from IGB Quickload main; update that text if needed; this will be for folders: https://data.bioviz.org/hotpollen/S_lycopersicum_Sep_2019/ and https://data.bioviz.org/hotpollen/S_lycopersicum_Jun_2022/. See quickload "main" for the text that's needed, and also the subversion repository
              * What the flavonoid RNA-Seq data folders contain, such as: https://data.bioviz.org/hotpollen/S_lycopersicum_Jun_2022/30-605730043/ and its sister directories

              Make a "zip" or "tar.gz" file with the HEADER.md files organized in a way that will make it easy for the person who deploys them on-line to put them in the right places and then view them. AL is probably going to be the person to deploy it all!

              For example, Ann thinks the easiest option for her would be to create a copy of the directory tree with folders needing HEADER.md files.               		The "hotpollen" IGB Quickload site at https://data.bioviz.org/hotpollen has several folders with data in them, but not a lot of description. We need to document this site a bit better on the site itself in preparation for submitting papers.

              For this task, add "HEADER.md" files that document:

              * What the SL5 June 2022 and SL4 Sep 2019 genomes are - use text from IGB Quickload main; update that text if needed; this will be for folders: https://data.bioviz.org/hotpollen/S_lycopersicum_Sep_2019/ and https://data.bioviz.org/hotpollen/S_lycopersicum_Jun_2022/. See quickload "main" for the text that's needed, and also the subversion repository
              * What the flavonoid RNA-Seq data folders contain, such as: https://data.bioviz.org/hotpollen/S_lycopersicum_Jun_2022/30-605730043/ and its sister directories; this would be like text from a methods section

              Make a "zip" or "tar.gz" file with the HEADER.md files organized in a way that will make it easy for the person who deploys them on-line to put them in the right places and then view them. AL is probably going to be the person to deploy it all!

              For example, Ann thinks the easiest option for her would be to create a copy of the directory tree with folders needing HEADER.md files.
              Mdavis4290 Molly Davis made changes -
              Sprint Fall 6 [ 182 ]
              Assignee Molly Davis [ molly ]
              Mdavis4290 Molly Davis made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
              Hide
              Permalink
              Mdavis4290 Molly Davis added a comment - - edited

              Genome Header Drafts: 

              <html>
<body>
<title>Hotpollen QuickLoad site for the tomato Solanum lycopersicum Experiments</title>
<h1>Solanum lycopersicum, SL5.0 Genome Experiments</h1>
<p>
The folders listed below contain data files for a specific experiment from our collaborators or NCBI experiments. 
Browser, available from <a href="https://bioviz.org">BioViz.org</a>.
</p>
<p>
These folders are: 

30-605730043/ (SRP not available yet?)
* Who it belongs to: Palanivelu, Ravishankar 
* Contact: rpalaniv@arizona.edu
* Experiment Introduction: Tamaulipas-pistils and heat stress over time

30-681594536/ (SRP not available yet?)
* Who it belongs to: Palanivelu, Ravishankar 
* Contact: rpalaniv@arizona.edu
* Experiment Introduction: Tomato varieties and heat stress over time

SRP100604/
* Who it belongs to: Huazhong Agricultural University
* Contact: bouy@mail.hzau.edu.cn
* Experiment Introduction: Profiling of drought-responsive microRNAand mRNA in tomato using high-throughput sequencing

SRP252265/
* Who it belongs to: Muday, Gloria
* Contact: gloria.muday@gmail.com
* Experiment Introduction: Genomic analysis of heat stress tolerance during tomato pollination

SRP268884/
* Who it belongs to: RWTH Aachen University
* Contact: awormit@bio1.rwth-aachen.de
* Experiment Introduction: Transcriptome of Solanum lycopersicum and Solanum pennellii under abiotic stresses

SRP328042/
* Who it belongs to: zhejiang university
* Contact: dandan yang
* Experiment Introduction: Morpho-Physiological and Transcriptome Changes in Tomato Anthers of Different Developmental Stages Under Drought Stress

mark-2022-timeseries/ (SRP441343) Check w/ Dr. Reid
* Who it belongs to: Brown University 
* Contact: mark_johnson_1@brown.edu
* Experiment Introduction: RNA-Seq of Solanum lycopersicum pollen tube under acute heat stress: A time series

muday-2022-timeseries/ (SRP460750) Check w/ Dr. Reid
* Who it belongs to: Muday, Gloria
* Contact: gloria.muday@gmail.com
* Experiment Introduction: Solanum lycopersicum RNA-Seq: Flavonols improve thermotolerance in tomato pollen during germination and tube elongation

seedlingPollen/ (SRP438952) Check w/ Dr. Reid
* Who it belongs to: 
* Contact: 
* Experiment Introduction: Heat stress tolerance during tomato pollination: Mature pollen and seedlings

</p>
</body>
</html>

              <html>
<body>
<title>Hotpollen QuickLoad site for the tomato Solanum lycopersicum Experiments</title>
<h1>Solanum lycopersicum, SL4.0 Genome Experiments</h1>
<p>
The folders listed below contain data files for a specific experiment from our collaborators or NCBI experiments. 
Browser, available from <a href="https://bioviz.org">BioViz.org</a>.
</p>
<p>
These folders are: 

30-605730043/ (SRP not available yet?)
* Who it belongs to: Palanivelu, Ravishankar 
* Contact: rpalaniv@arizona.edu
* Experiment Introduction: Tamaulipas-pistils and heat stress over time

30-681594536/ (SRP not available yet?)
* Who it belongs to: Palanivelu, Ravishankar 
* Contact: rpalaniv@arizona.edu
* Experiment Introduction: Tomato varieties and heat stress over time

30-804059537/ (SRP not available yet?)
* Who it belongs to: Palanivelu, Ravishankar 
* Contact: rpalaniv@arizona.edu
* Experiment Introduction: Tomato varieties and heat stress over time


ARE/
* Who it belongs to: Muday, Gloria
* Contact: gloria.muday@gmail.com
* Experiment Introduction: Genomic analysis of heat stress tolerance during tomato pollination

annots.xml
genome.txt
hisat2_bams/
muday-2022-timeseries/ (SRP460750)
* Who it belongs to: Muday, Gloria
* Contact: gloria.muday@gmail.com
* Experiment Introduction: Genomic analysis of heat stress tolerance during tomato pollination
</p>
</body>
</html>

              Notes about directories:

              • SL5 tomato: doesn't include Ravi 30-804059537 data
              • Some directories need to be updated and renamed because the SRP names are available now and new output files could be added as well from cluster
              • Need to double check contacts because SRA submissions don't include them
              • SRP252265 belongs to who?
              Show
              Mdavis4290 Molly Davis added a comment - - edited Genome Header Drafts : SL5 header = https://data.bioviz.org/hotpollen/S_lycopersicum_Jun_2022/ <html> <body> <title>Hotpollen QuickLoad site for the tomato Solanum lycopersicum Experiments</title> <h1>Solanum lycopersicum, SL5.0 Genome Experiments</h1> <p> The folders listed below contain data files for a specific experiment from our collaborators or NCBI experiments. Browser, available from <a href= "https: //bioviz.org" >BioViz.org</a>. </p> <p> These folders are: 30-605730043/ (SRP not available yet?) * Who it belongs to: Palanivelu, Ravishankar * Contact: rpalaniv@arizona.edu * Experiment Introduction: Tamaulipas-pistils and heat stress over time 30-681594536/ (SRP not available yet?) * Who it belongs to: Palanivelu, Ravishankar * Contact: rpalaniv@arizona.edu * Experiment Introduction: Tomato varieties and heat stress over time SRP100604/ * Who it belongs to: Huazhong Agricultural University * Contact: bouy@mail.hzau.edu.cn * Experiment Introduction: Profiling of drought-responsive microRNAand mRNA in tomato using high-throughput sequencing SRP252265/ * Who it belongs to: Muday, Gloria * Contact: gloria.muday@gmail.com * Experiment Introduction: Genomic analysis of heat stress tolerance during tomato pollination SRP268884/ * Who it belongs to: RWTH Aachen University * Contact: awormit@bio1.rwth-aachen.de * Experiment Introduction: Transcriptome of Solanum lycopersicum and Solanum pennellii under abiotic stresses SRP328042/ * Who it belongs to: zhejiang university * Contact: dandan yang * Experiment Introduction: Morpho-Physiological and Transcriptome Changes in Tomato Anthers of Different Developmental Stages Under Drought Stress mark-2022-timeseries/ (SRP441343) Check w/ Dr. Reid * Who it belongs to: Brown University * Contact: mark_johnson_1@brown.edu * Experiment Introduction: RNA-Seq of Solanum lycopersicum pollen tube under acute heat stress: A time series muday-2022-timeseries/ (SRP460750) Check w/ Dr. Reid * Who it belongs to: Muday, Gloria * Contact: gloria.muday@gmail.com * Experiment Introduction: Solanum lycopersicum RNA-Seq: Flavonols improve thermotolerance in tomato pollen during germination and tube elongation seedlingPollen/ (SRP438952) Check w/ Dr. Reid * Who it belongs to: * Contact: * Experiment Introduction: Heat stress tolerance during tomato pollination: Mature pollen and seedlings </p> </body> </html> SL4 header = https://data.bioviz.org/hotpollen/S_lycopersicum_Sep_2019/ <html> <body> <title>Hotpollen QuickLoad site for the tomato Solanum lycopersicum Experiments</title> <h1>Solanum lycopersicum, SL4.0 Genome Experiments</h1> <p> The folders listed below contain data files for a specific experiment from our collaborators or NCBI experiments. Browser, available from <a href= "https: //bioviz.org" >BioViz.org</a>. </p> <p> These folders are: 30-605730043/ (SRP not available yet?) * Who it belongs to: Palanivelu, Ravishankar * Contact: rpalaniv@arizona.edu * Experiment Introduction: Tamaulipas-pistils and heat stress over time 30-681594536/ (SRP not available yet?) * Who it belongs to: Palanivelu, Ravishankar * Contact: rpalaniv@arizona.edu * Experiment Introduction: Tomato varieties and heat stress over time 30-804059537/ (SRP not available yet?) * Who it belongs to: Palanivelu, Ravishankar * Contact: rpalaniv@arizona.edu * Experiment Introduction: Tomato varieties and heat stress over time ARE/ * Who it belongs to: Muday, Gloria * Contact: gloria.muday@gmail.com * Experiment Introduction: Genomic analysis of heat stress tolerance during tomato pollination annots.xml genome.txt hisat2_bams/ muday-2022-timeseries/ (SRP460750) * Who it belongs to: Muday, Gloria * Contact: gloria.muday@gmail.com * Experiment Introduction: Genomic analysis of heat stress tolerance during tomato pollination </p> </body> </html> Notes about directories: SL5 tomato: doesn't include Ravi 30-804059537 data Some directories need to be updated and renamed because the SRP names are available now and new output files could be added as well from cluster Need to double check contacts because SRA submissions don't include them SRP252265 belongs to who?
              Mdavis4290 Molly Davis made changes -
              Story Points 0.5 3
              Hide
              Permalink
              Mdavis4290 Molly Davis added a comment - - edited

              RNA-Seq data folders Draft: 

              <html>
<body>
<title>Hotpollen QuickLoad site for the tomato Solanum lycopersicum Experiments</title>
<h1>Solanum lycopersicum, IGB Data Files</h1>
<p>
The following data files are a result of using a Nextflow nf-core pipeline and personal scripts. The  nf-core/rnaseq bioinformatics pipeline was used to analyse RNA sequencing data obtained from organisms with a reference genome and annotation. It takes a samplesheet and FASTQ files as input, performs quality control (QC), trimming and (pseudo-)alignment, and produces a gene expression matrix and extensive QC report. The results after the star_salmon alignment includes BAM and counts files. The counts files (counts.tsv) can be used to analyze the data. The BAM files can be used to create visualizations in IGB but some other files needed to be made first before using them in IGB. The scripts used create coverage graphs (.scaled.bedgraph) and junction files (.FJ.bed). The pipeline and scripts were created on the UNC Charlotte HPC cluster. The final data can be seen here which is configured for visualization in the Integrated Genome Browser (link).

The folders listed below contain:

.FJ.bed.gz
.FJ.bed.gz.tbi
.bam
.bam.bai
.scaled.bedgraph.gz
.scaled.bedgraph.gz.tbi
-salmon.merged.gene_counts.tsv
</p>
</body>
</html>
              Show
              Mdavis4290 Molly Davis added a comment - - edited RNA-Seq data folders Draft : <html> <body> <title>Hotpollen QuickLoad site for the tomato Solanum lycopersicum Experiments</title> <h1>Solanum lycopersicum, IGB Data Files</h1> <p> The following data files are a result of using a Nextflow nf-core pipeline and personal scripts. The nf-core/rnaseq bioinformatics pipeline was used to analyse RNA sequencing data obtained from organisms with a reference genome and annotation. It takes a samplesheet and FASTQ files as input, performs quality control (QC), trimming and (pseudo-)alignment, and produces a gene expression matrix and extensive QC report. The results after the star_salmon alignment includes BAM and counts files. The counts files (counts.tsv) can be used to analyze the data. The BAM files can be used to create visualizations in IGB but some other files needed to be made first before using them in IGB. The scripts used create coverage graphs (.scaled.bedgraph) and junction files (.FJ.bed). The pipeline and scripts were created on the UNC Charlotte HPC cluster. The final data can be seen here which is configured for visualization in the Integrated Genome Browser (link). The folders listed below contain: .FJ.bed.gz .FJ.bed.gz.tbi .bam .bam.bai .scaled.bedgraph.gz .scaled.bedgraph.gz.tbi -salmon.merged.gene_counts.tsv </p> </body> </html>
              Mdavis4290 Molly Davis made changes -
              Sprint Fall 6 [ 182 ] Fall 7 [ 183 ]
              Mdavis4290 Molly Davis made changes -
              Status In Progress [ 3 ] To-Do [ 10305 ]
              Mdavis4290 Molly Davis made changes -
              Sprint Fall 7 [ 183 ]

                People

                • Assignee:
                  Mdavis4290 Molly Davis
                  Reporter:
                  ann.loraine Ann Loraine
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                  • Created:
                    Updated: