I downloaded the Nov. 2020 (mRatBN7.2/rn7) assembly of the rat genome (rn7) 2bit file from https://hgdownload.soe.ucsc.edu/goldenPath/rn7/bigZips/

I pulled the rat info from gene2accession file using NCBI txid 10116

gunzip -c gene2accession.gz | grep '^10116\t' > ~/Desktop/jiraIssues/3362/10116.gene2accession.txt

I created bed 14 files for UCSC refGene and NCBI Ref Seq (ncbiRefSeq):

ucscToBedDetail.py -a 10116.gene2accession.txt -g Rattus_norvegicus.gene_info R_norvegicus_Nov_2020_refGene.bed.gz R_norvegicus_Nov_2020_refGene.bed

ucscToBedDetail.py -a 10116.gene2accession.txt -g Rattus_norvegicus.gene_info R_norvegicus_Nov_2020_ncbiRefSeq.bed.gz R_norvegicus_Nov_2020_ncbiRefSeq.bed

I then sorted, bgzipped, and tabix indexed the two bed files:

sort -k1,1 -k2,2n R_norvegicus_Nov_2020_refGene.bed | bgzip > R_norvegicus_Nov_2020_refGene.bed.gz
tabix -0 -s 1 -b 2 -e 3 R_norvegicus_Nov_2020_refGene.bed.gz

sort -k1,1 -k2,2n R_norvegicus_Nov_2020_ncbiRefSeq.bed | bgzip > R_norvegicus_Nov_2020_ncbiRefSeq.bed.gz
tabix -0 -s 1 -b 2 -e 3 R_norvegicus_Nov_2020_ncbiRefSeq.bed.gz

Next I sorted, bgzipped, and tabix indexed the psl files for all_est and all_mrna:

gunzip \-c R_norvegicus_Nov_2020_all_est.psl.gz | grep -v bin | cut -f2- > R_norvegicus_Nov_2020_all_est.psl
sort -k14,14 -k16,16n R_norvegicus_Nov_2020_all_est.psl > sorted.psl
mv sorted.psl R_norvegicus_Nov_2020_all_est.psl
bgzip R_norvegicus_Nov_2020_all_est.psl
tabix -s 14 -b 16 -0 R_norvegicus_Nov_2020_all_est.psl.gz

gunzip \-c R_norvegicus_Nov_2020_all_mrna.psl.gz | grep -v bin | cut -f2- > R_norvegicus_Nov_2020_all_mrna.psl
sort -k14,14 -k16,16n R_norvegicus_Nov_2020_all_mrna.psl > sorted.psl
mv sorted.psl R_norvegicus_Nov_2020_all_mrna.psl
bgzip R_norvegicus_Nov_2020_all_mrna.psl
tabix -s 14 -b 16 -0 R_norvegicus_Nov_2020_all_mrna.psl.gz

I have placed the rn7 quickload in CyVerse for testing.

To test:
In IGB,

1. Add https://data.cyverse.org/dav-anon/iplant/home/nowlanf/rat_2020/quickload as a new Data Source in IGB (IntegratedGenomeBrowser > Settings > Data Sources > Add...).
2. Select the Rattus norvegicus Species and the R_norvegicus_Nov_2020 Genome Version.
3. The RefGene track should appear and should automatically load data.
4. Navigate to: chr1:202,781,726-202,796,554
5. Click Load Sequence.
6. Residues (ATCG) should load (may take a little while, CyVerse can be slow).
7. Check that there are no errors in the log.
8. Under Available Data in the Data Access tab, click the checkbox for mRNA, EST, and NCBI RefSeq
9. Click Load Data
10. Gene annotations for each track should load.
11. Check that there are no errors in the log.
12. Check that the UCSC (DAS) folder appears under Available Data in the Data Access tab.
13. Click the checkbox for ncbiRefSeqCurated.
14. Click Load Data.
15. Check that there are no errors in the log.

Testing: All data loaded correctly and I ran into no errors in the log. Good Job!

Notes from pushing changes to subversion repository: https://svn.bioviz.org/viewvc/genomes/quickload/R_norvegicus_Nov_2020/

Comment for subversion update
IGBF-3362: Add Rattus norvegicus Nov 2020 genome;Jun 29, 2023

Need to update the following files:
contents.txt -> R_norvegicus_Nov_2020 Rattus norvegicus (Nov 2020) rat (mRatBN7.2/rn7)
.htaccess -> AddDescription "Rattus norvegicus (Nov 2020) rat (mRatBN7.2/rn7)" R_norvegicus_Nov_2020

Basic steps to checking in files and adding new rat folder with files:

1. Modify the contentx.txt and .htaccess files
2. Drag the rat folder into the quickload folder
   then:

   svn status
   svn ci -m "IGBF-3362: Add Rattus norvegicus Nov 2020 genome;Jun 29, 2023" quickload/.htaccess
   svn ci -m "IGBF-3362: Add Rattus norvegicus Nov 2020 genome;Jun 29, 2023" quickload/contents.txt
   svn add quickload/R_norvegicus_Nov_2020
   svn ci -m "IGBF-3362: Add Rattus norvegicus Nov 2020 genome;Jun 29, 2023"
   

New rat genome has been added to subversion repository.

Next step, deploy to quickload site.

Confirming new genome is added to the repository by viewing this following links to the subversion repository web application "viewvc":

• https://svn.bioviz.org/viewvc/genomes/quickload/contents.txt?view=log.
• https://svn.bioviz.org/viewvc/genomes/quickload/contents.txt?annotate=175

Thank you Nowlan Freese for including the ticket number in the commit message.

FYI:

Note to Nowlan Freese:

• If UCSC is hosting a 2bit file for this genome on a standard HTTP or HTTPS host, you do not need to version-control the file. This is because IGB's later versions can access the 2bit file via a URL. That feature was added in the ticket titled "Enable Quickload to specify the 2bit file for a genome" .

I think this latest revision for the IGB Quickload subversion repository is fine. I will update the IGB Quickload hosts now.

The two IGB is using currently:

• the "scidas" host, running on RENCI resources, with Quickload URL: http://lorainelab-quickload.scidas.org/quickload/
• the "igbquickload.org" host, running on Amazon (to be replaced by UNC Charlotte infrastructure shortly.) with Quickload URL: http://igbquickload.org/quickload/

Also checked that the ".htaccess" file is updated. It is updated.

New data are deployed to the above hosts. Ready for testing.

attn: Nowlan Freese

The new mouse and rat data are deployed.

Tested on Mac on IGB release (9.1.10).
Able to load all data (RefGene, NCBI RefSeq, mRNA, EST, sequence file) on scidas and igbquickload.org

Closing ticket.