[IGBF-3892] Add Vanessa cardui genome to IGB - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
None

Story Points:
1
Epic Link:
Add genomes requested during SDB
Sprint:
Fall 7

Description

Task: Add the Vanessa cardui genome and annotation to IGB.

Link to genome on NCBI: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_905220365.1/

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Issue Links

relates to

IGBF-4038 Improve documentation description quickload files for painted lady genome assembly

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Paige Kulzer added a comment - 20/Sep/24 8:22 AM

Below is an outline of the steps I followed to create this Quickload:

1.Use wget to obtain the .2bit file from UCSC's track hub directory, then rename it

wget https://hgdownload.soe.ucsc.edu/hubs/GCF/905/220/365/GCF_905220365.1/GCF_905220365.1.2bit
mv GCF_905220365.1.2bit ilVanCard2.1.2bit

2. Create genome.txt, then check that the chromosome's are ordered logically (i.e., numerically)

./twoBitInfo ilVanCard2.1.2bit genome.txt
cat genome.txt

3. Use Vanessa cardui's taxID (171605) to get the information needed from gene2accession.gz and gene_info.gz to create the BED14 file in a later step

gunzip -c gene2accession.gz | grep '^171605\t' > 171605.gene2accession.txt
gunzip -c gene_info.gz | grep '^171605\t' > 171605.gene_info.txt

4. Download the RefSeqAll BED file from UCSC's table browser (Link: https://genome.ucsc.edu/cgi-bin/hgTables), then create the BED14 file using the following code:

cd ~/Documents/Repos/genomesource/
./ucscToBedDetail.py -a ~/Downloads/171605.gene2accession.txt -g ~/Downloads/171605.gene_info.txt ~/Downloads/V_cardui_ncbiRefSeq.bed.gz ~/Downloads/V_cardui_Feb_2021_ncbiRefSeq.bed

5. Sort, gzip, and tabix the BED14 file

cd ~/Downloads/
sort -k1,1 -k2,2n V_cardui_Feb_2021_ncbiRefSeq.bed | bgzip > V_cardui_Feb_2021_ncbiRefSeq.bed.gz
tabix -0 -s 1 -b 2 -e 3 V_cardui_Feb_2021_ncbiRefSeq.bed.gz

6. Sanity check the 2bit and BED files - Add the 2bit file as a reference, then drag/drop the BED files into IGB. Confirm that gene models are present, labeled correctly, and that no error messages are present in the Log.

7. Create a new directory in the quickload repo, then create annots.xml

cd ~/Documents/Repos/quickload/
svn mkdir V_cardui_Feb_2021
svn cp A_gambiae_Feb_2003/annots.xml V_cardui_Feb_2021
nano V_cardui_Feb_2021/annots.xml

8. Add V_cardui_Feb_2021 to contents.txt and .htaccess

nano contents.txt

V_cardui_Feb_2021 Vanessa cardui (Feb 2021) painted lady (ilVanCard2.1)

nano .htaccess

AddDescription "Vanessa cardui (Feb 2021) painted lady (ilVanCard2.1)" V_cardui_Feb_2021

9. Create HEADER.md

../genomesource/writeQuickLoadHeaderUCSC.py V_cardui_Feb_2021 > V_cardui_Feb_2021/HEADER.md

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Paige Kulzer added a comment - 20/Sep/24 8:22 AM Below is an outline of the steps I followed to create this Quickload: 1.Use wget to obtain the .2bit file from UCSC's track hub directory, then rename it wget https: //hgdownload.soe.ucsc.edu/hubs/GCF/905/220/365/GCF_905220365.1/GCF_905220365.1.2bit mv GCF_905220365.1.2bit ilVanCard2.1.2bit 2. Create genome.txt, then check that the chromosome's are ordered logically (i.e., numerically) ./twoBitInfo ilVanCard2.1.2bit genome.txt cat genome.txt 3. Use Vanessa cardui 's taxID (171605) to get the information needed from gene2accession.gz and gene_info.gz to create the BED14 file in a later step gunzip -c gene2accession.gz | grep '^171605\t' > 171605.gene2accession.txt gunzip -c gene_info.gz | grep '^171605\t' > 171605.gene_info.txt 4. Download the RefSeqAll BED file from UCSC's table browser (Link: https://genome.ucsc.edu/cgi-bin/hgTables ), then create the BED14 file using the following code: cd ~/Documents/Repos/genomesource/ ./ucscToBedDetail.py -a ~/Downloads/171605.gene2accession.txt -g ~/Downloads/171605.gene_info.txt ~/Downloads/V_cardui_ncbiRefSeq.bed.gz ~/Downloads/V_cardui_Feb_2021_ncbiRefSeq.bed 5. Sort, gzip, and tabix the BED14 file cd ~/Downloads/ sort -k1,1 -k2,2n V_cardui_Feb_2021_ncbiRefSeq.bed | bgzip > V_cardui_Feb_2021_ncbiRefSeq.bed.gz tabix -0 -s 1 -b 2 -e 3 V_cardui_Feb_2021_ncbiRefSeq.bed.gz 6. Sanity check the 2bit and BED files - Add the 2bit file as a reference, then drag/drop the BED files into IGB. Confirm that gene models are present, labeled correctly, and that no error messages are present in the Log. 7. Create a new directory in the quickload repo, then create annots.xml cd ~/Documents/Repos/quickload/ svn mkdir V_cardui_Feb_2021 svn cp A_gambiae_Feb_2003/annots.xml V_cardui_Feb_2021 nano V_cardui_Feb_2021/annots.xml 8. Add V_cardui_Feb_2021 to contents.txt and .htaccess nano contents.txt V_cardui_Feb_2021 Vanessa cardui (Feb 2021) painted lady (ilVanCard2.1) nano .htaccess AddDescription "Vanessa cardui (Feb 2021) painted lady (ilVanCard2.1)" V_cardui_Feb_2021 9. Create HEADER.md ../genomesource/writeQuickLoadHeaderUCSC.py V_cardui_Feb_2021 > V_cardui_Feb_2021/HEADER.md

5 older comments

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Nowlan Freese added a comment - 20/Dec/24 10:29 AM

Paige Kulzer - the 2bit file has a weird name and isn't loading correctly, can you update it to V_cardui_Feb_2021.2bit and push it to the SVN repo then ask Dr. Loraine to deploy it?

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Nowlan Freese added a comment - 20/Dec/24 10:29 AM Paige Kulzer - the 2bit file has a weird name and isn't loading correctly, can you update it to V_cardui_Feb_2021.2bit and push it to the SVN repo then ask Dr. Loraine to deploy it?

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Paige Kulzer added a comment - 20/Dec/24 10:42 AM

Ann Loraine, as per Nowlan's comment above, I've updated the 2bit files name to "V_cardui_Feb_2021.2bit" and have pushed it to the SVN repo. It's ready for you to deploy!

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Paige Kulzer added a comment - 20/Dec/24 10:42 AM Ann Loraine , as per Nowlan's comment above, I've updated the 2bit files name to "V_cardui_Feb_2021.2bit" and have pushed it to the SVN repo. It's ready for you to deploy!

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Ann Loraine added a comment - 21/Dec/24 9:08 AM

Update:

New file is deployed and old one is deleted - I updated quickloads hosted at RENCI and UNC Charlotte

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Ann Loraine added a comment - 21/Dec/24 9:08 AM Update: New file is deployed and old one is deleted - I updated quickloads hosted at RENCI and UNC Charlotte

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Ann Loraine added a comment - 21/Dec/24 9:21 AM - edited

Testing:

It looks like the documentation describing the data files needs to be improved.

The description of the files and where they came from in the comments above don't match the documentation. Specifically, the origin of the files is different. It looks like we got the files from the UCSC Genome Informations Web site and then used our tools to convert them to our preferred formats.

Suggestion:

Since we are doing a pretty good job of describing our process in the comments above (thanks Paige Kulzer) could we simply link to this ticket from our header file?

We could provide some very generic – but accurate – descriptions of where the files came from and how we processed them. We could also then provide a direct link to this Jira ticket, which should be publicly accessible.

I recommend we maybe make "Improve documentation for painted lady genome assembly quickload" as a new ticket.

Once that documentation is more complete, we could then get in touch with researchers working with this assembly and get their input. Also, we should make sure to link to articles for this particular genome assembly so that users will be able to get more information.

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Ann Loraine added a comment - 21/Dec/24 9:21 AM - edited Testing: It looks like the documentation describing the data files needs to be improved. The description of the files and where they came from in the comments above don't match the documentation. Specifically, the origin of the files is different. It looks like we got the files from the UCSC Genome Informations Web site and then used our tools to convert them to our preferred formats. Suggestion: Since we are doing a pretty good job of describing our process in the comments above (thanks Paige Kulzer ) could we simply link to this ticket from our header file? We could provide some very generic – but accurate – descriptions of where the files came from and how we processed them. We could also then provide a direct link to this Jira ticket, which should be publicly accessible. I recommend we maybe make "Improve documentation for painted lady genome assembly quickload" as a new ticket. Once that documentation is more complete, we could then get in touch with researchers working with this assembly and get their input. Also, we should make sure to link to articles for this particular genome assembly so that users will be able to get more information.

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Ann Loraine added a comment - 21/Dec/24 9:47 AM

I made the recommend ticket for improving the genome assembly documentation. Closing this one now.

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Ann Loraine added a comment - 21/Dec/24 9:47 AM I made the recommend ticket for improving the genome assembly documentation. Closing this one now.

People

Assignee:

Paige Kulzer

Reporter:

Paige Kulzer

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Watchers:

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Dates

Created:

05/Sep/24 1:52 PM

Updated:

21/Dec/24 9:47 AM

Resolved:

21/Dec/24 9:47 AM