Improve the gene description for the ARE gene in SL4 and SL5 annotations

Ann Loraine added a comment - 21/May/24 9:45 AM Request for Paige Kulzer : Please transfer your comment on what you would like to see done (from your email from yesterday or last week?)

Paige Kulzer added a comment - 21/May/24 9:49 AM Can we please add keywords such as "F3H" and "flavanone 3-hydroxylase" to the gene annotations labeled "PRAM_26184.1" in SL5 and "solyc02g083860" in SL4? This will allow me to quickly search for and locate the gene where the point mutation occurs in the are genotype.

Ann Loraine added a comment - 22/May/24 8:04 AM - edited Added requested text to the description field in SL4 and SL5 annotation files. To test, confirm that when you open these genomes, you can locate the "are" locus by searching F3H.

Paige Kulzer added a comment - 22/May/24 9:24 AM Please fix the following spelling error: hydroxlase -> hydrox y lase

Ann Loraine added a comment - 26/May/24 12:14 PM - edited Annotation description change process: Update IGB quickload local copy to get most up-to-date version of the repository cd quickload svn up extract line for PRAM_26184.1 and save to a temp file gunzip -c S_lycopersicum_Jun_2022.bed.gz | grep PRAM_26184.1 > txt.bed Edit txt.bed to contain text we want to use instead: anthocyanin-reduced (are) flavanone 3-hydroxylase (F3H) SL4:Solyc02g083860 Create new bed file lacking info lacking line for F3H gene (will be replaced in future step): gunzip -c S_lycopersicum_Jun_2022.bed.gz | grep -v PRAM_26184.1 > S_lycopersicum_Jun_2022.bed Check it has the right number of lines: local aloraine$ gunzip -c S_lycopersicum_Jun_2022.bed.gz | wc -l 43752 local aloraine$ wc -l S_lycopersicum_Jun_2022.bed 43751 S_lycopersicum_Jun_2022.bed It's all good. Add new text to new file: cat txt.bed S_lycopersicum_Jun_2022.bed | sort -k1,1 -k2,2n | bgzip > S_lycopersicum_Jun_2022.bed.gz Check my work: gunzip -c S_lycopersicum_Jun_2022.bed.gz | diff - S_lycopersicum_Jun_2022.bed 17845d17844 < 2 47448952 47451152 PRAM_26184.1.p1 0 - 47449290 47451066 0 3 638,429,446, 0,706,1754, PRAM_26184 anthocyanin-reduced (are) flavanone 3-hydroxylase (F3H) SL4:solyc02g083860 The new file contains the newly crafted line for the gene. Create a new index: local aloraine$ tabix -s 1 -b 2 -e 3 S_lycopersicum_Jun_2022.bed.gz local aloraine$ New index is made. All is good. Added to the repository: local aloraine$ svn ci S_lycopersicum_Jun_2022.bed.gz S_lycopersicum_Jun_2022.bed.gz.tbi -m "IGBF-3712 Improve gene description for anthocyanin-reduced (are) in SL5" Sending S_lycopersicum_Jun_2022.bed.gz Sending S_lycopersicum_Jun_2022.bed.gz.tbi Transmitting file data ..done Committing transaction... Committed revision 189.

Ann Loraine added a comment - 28/May/24 1:40 PM - edited Do the above, but for SL4: gunzip -c S_lycopersicum_Sep_2019.bed.gz | grep Solyc02g083860 > txt.bed Edit txt.bed; replace final field with text: anthocyanin-reduced (are) flavanone 3-hydroxylase (F3H) Replace old line with new one and make tabix index: gunzip -c S_lycopersicum_Sep_2019.bed.gz | grep -v Solyc02g083860 > S_lycopersicum_Sep_2019.bed cat txt.bed S_lycopersicum_Sep_2019.bed | sort -k1,1 -k2,2n | bgzip > S_lycopersicum_Sep_2019.bed.gz Make index, with special options: local aloraine$ tabix -s 1 -b 2 -e 3 S_lycopersicum_Sep_2019.bed.gz [W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option? local aloraine$ tabix -s 1 -b 2 -e 3 -0 S_lycopersicum_Sep_2019.bed.gz [tabix] the index file exists. Please use '-f' to overwrite. local aloraine$ tabix -s 1 -b 2 -e 3 -0 -f S_lycopersicum_Sep_2019.bed.gz

Ann Loraine added a comment - 28/May/24 1:52 PM New files are now available in subversion repository version 191 and above.

Ann Loraine added a comment - 28/May/24 1:53 PM Review the gene descriptions for the gene in SL4 and SL5. If it's OK, move to Done.

Paige Kulzer added a comment - 30/May/24 9:59 AM The spelling error has been corrected. I was able to search for this gene and find it easily in both SL4 and SL5. Moving to Done.