Page History

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• choose assembly using release date to match it with IGB QuickLoad genome version
• choose group: mRNA and EST tracks
• choose track: SPECIES mRNA
• choose table: all_mrna
• choose output format: selected fields from primary and related tables
• enter output file G_species_MMM_YYYY_all_mrna.bedpsl.gz
  • The prefix should be THE SAME AS the genome version directory name, with _all_mrna appended.
• file type returned: choose gzip compressed

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$ gunzip -c ~/Downloads/G_species_MMM_YYYY_all_mrna.bedpsl.gz | grep -v '^#' | sort -k14,14 -k16,16n | bgzip > G_species_MMM_YYYY_all_mrna.psl.gz

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Make sure the number of chromosomes listedin listed in the file does not exceed the number of chromosomes listed in the genome descriptor file genome.txt:

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The first line counts the number of unique sequences appearing the first column of the bed file. The second line counts the number of lines in the genome.txt file. They should be the same.

Edit annots.xml

The annots.xml file description for the all_mrna annotations contains the date the data were downloaded. Edit the file accordingly to reflect today's date.

Annots.xml attributes:

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title	mRNA
description	UCSC all mRNA track (date of download)
url	http://www.igbquickload.org/quickload/G_species_MMM_YYYYImage Added

All other attributes (e.g., foreground, background, load_hint) should match other UCSC genome release mRNA data sets.

Check in the new files

Use svn status command to double-check which files you've changed:

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Check in the files one-by-one:

svn ci G_species_MMM_YYYY_refGene.bed.gz -m "Enter a message here."
svn ci G_species_MMM_YYYY_refGene.bed.gz.tbi -m "Enter a message here."
svn ci annots.xml -m "Enter a message here."

The message you enter should include the date of the download. This is important because researchers who are using these data will need to know this information in order to publish their results.

Update all_est

Repeat the same steps you used for all_mrna, but instead of choosing Track: SPECIES mRNAs, instead choose SPECIES ESTs, and choose table all_ests.

The data files you create will contain table suffix all_est, e.g., G_species_MMM_YYYY_all_est.psl.gz and its index G_species_MMM_YYYY_all_est.psl.gz.tbi.

The data set file name, title, and description in the annots.xml should be:

file name: G_species_MMM_YYYY_all_est.psl.gz
title: EST
description: UCSC all EST track (date of download)
url: http://www.igbquickload.org/G_species_MMM_YYYY^{Image Added}