[IGBF-3362] Add rn7 rat genome to IGB - JIRA UNCC

Details

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

Story Points:
2
Epic Link:
Improve IGB for users
Sprint:
Summer 4 2023 June 26

Description

Situation: The most recent rat genome (rn7) is not currently available in IGB.

Task: Add the rn7 rat genome to IGB: https://hgdownload.soe.ucsc.edu/downloads.html#rat

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relates to

IGBF-3330 Add mm39 (GRCm39) mouse genome to IGB

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Nowlan Freese added a comment - 28/Jun/23 3:28 PM - edited

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

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Nowlan Freese added a comment - 28/Jun/23 3:28 PM - edited 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

6 older comments

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Ann Loraine added a comment - 07/Jul/23 3:12 PM - edited

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/

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Ann Loraine added a comment - 07/Jul/23 3:12 PM - edited 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/

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Ann Loraine added a comment - 07/Jul/23 3:17 PM

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

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Ann Loraine added a comment - 07/Jul/23 3:17 PM Also checked that the ".htaccess" file is updated. It is updated.

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Ann Loraine added a comment - 07/Jul/23 3:22 PM

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

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Ann Loraine added a comment - 07/Jul/23 3:22 PM New data are deployed to the above hosts. Ready for testing.

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Ann Loraine added a comment - 07/Jul/23 3:22 PM

attn: Nowlan Freese

The new mouse and rat data are deployed.

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Ann Loraine added a comment - 07/Jul/23 3:22 PM attn: Nowlan Freese The new mouse and rat data are deployed.

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Nowlan Freese added a comment - 07/Jul/23 4:27 PM

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.

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Nowlan Freese added a comment - 07/Jul/23 4:27 PM 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.

People

Assignee:

Nowlan Freese

Reporter:

Nowlan Freese

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Watchers:

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Dates

Created:

08/Jun/23 11:04 AM

Updated:

07/Jul/23 4:29 PM

Resolved:

07/Jul/23 4:29 PM