Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:0.25
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Epic Link:
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Sprint:Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 1 2022 Aug 15, Fall 2 2022 Sep 5, Fall 3 2022 Sep 26, Fall 4 2022 Oct 10, Fall 5 2022 Oct 24, Fall 6 2022 Nov 7
Description
Git repository for this sub-project: https://bitbucket.org/hotpollen/splicing-analysis/src/master/
Use gene mapping table to add gene descriptions to new annotations bed-detail file for SL5.0 genome assembly release and annotations.
Specifically:
- Get the BED-detail gene model file from IGBQuickload repository: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Jun_2022/S_lycopersicum_Jun_2022.bed.gz
The 13th column of this file contains a gene identifier. The 4th column contains a transcript identifier. The final (14th) column contains "NA" for "Not Available." We would like it to instead contain a description of the gene. Since we don't have that, we would like to insert the description of gene counterparts present in the SL4.0 annotations.
- Note that the SL4 annotations can be found here: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Sep_2019/S_lycopersicum_Sep_2019.bed.gz
To map genes from SL4 onto SL5, you need a mapping file. The people who made SL5.0 gave us that mapping file back in July 2022:
Dear Ann,
Yes, we do have tables for the conversion between different versions. They are now avaiable on our website (http://solomics.agis.org.cn/tomato/ftp/ID_convert/).
Thanks so much for the intergration! I would be happy to forward it to my colleagues when it is avaiable.
Best regards,
Yao
Mapping files needed are also available in: /nobackup/tomato_genome/alt_splicing/mappingfiles
Attachments
Issue Links
Activity
Update:
- Aligned SL4 gene models onto SL5 genome assembly using blat.sh:
#!/bin/bash G=S_lycopersicum_Jun_2022 D=$G.2bit Q=S_lycopersicum_Sep_2019_models_cDNA.fa PSL=SL42SL5.psl MI=15000 blat -noTrimA -maxIntron=$MI -noHead -minIdentity=95 -dots=100 $D $Q $PSL
- Sorted and tabix-indexed PSL output file with:
sort -k14,14 -k16,16n SL42SL5.psl | bgzip -c > SL42SL5.psl.gz tabix -s 14 -b 16 -e 17 SL42SL5.psl.gz
- Added output and code to repository - bitbucket.org/hotpollen/splicing-analysis.git
Reference: https://bitbucket.org/lorainelab/affyprobesetsforigb/src/master/ (documents how to make a tabix-indexed file from PSL blat output)
Update:
Modifying SL5 description field to include SL4 locus identifier, for example:
hexokinase-1 protein (AHRD V3.3 *** AT1G05205.1)
becomes:
hexokinase-1 protein (AHRD V3.3 *** AT1G05205.1) ITAG4.0:Solyc07g052420.3
Added new file to svn repository after creating tabix-indexed file with:
sort -k1,1 -k2,2n ~/src/splicing-analysis2/DescriptionMapping/output/S_lycopersicum_Jun_2022.bed | bgzip > S_lycopersicum_Jun_2022.bed.gz tabix -s 1 -b 2 -e 3 S_lycopersicum_Jun_2022.bed.gz
svn repo info:
- Browse by visiting https://svn.bioviz.org/viewvc/
- svn repo URLs:
URL: https://svn.bioviz.org/repos/genomes/quickload/S_lycopersicum_Jun_2022
Repository Root: https://svn.bioviz.org/repos/genomes - to check out the repo using read-only user, enter user name "guest" password "guest"
Updated quickload sites on RENCI and UNCC hosting.
At UNCC, logged in with:
ssh -J aloraine@cci-jump.uncc.edu -p 1657 aloraine@igbquickload.org
At RENCI, logged in with:
ssh -J aloraine@hop.renci.org aloraine@lorainelab-quickload.scidas.org
Potentially useful code is available here:
Check out the code used to read the BED annotation files.