Commits for vsmalladi
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v266_preview2 to v266_base (2012-04-17 to 2012-04-24) v266
- Feedback from NHGRI has indicated that tracks should be named Repli-chip rather than Repli-seq. Redmine #6226, #6627.
- src/hg/encode/DAFs/3.0/hg19/wgEncodeFsuRepliChip.daf - lines changed 41, context: html, text, full: html, text
- src/hg/encode/DAFs/3.0/hg19/wgEncodeFsuRepliSeq.daf - lines changed 41, context: html, text, full: html, text
- src/hg/encode/DAFs/3.0/mm9/wgEncodeFsuRepliChip.daf - lines changed 44, context: html, text, full: html, text
- src/hg/encode/DAFs/3.0/mm9/wgEncodeFsuRepliSeq.daf - lines changed 44, context: html, text, full: html, text
- src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 7, context: html, text, full: html, text
- Changed RepliSeq to Repli-chip. Redmine #6626.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeFsuRepliChip.ra - lines changed 406, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeFsuRepliSeq.ra - lines changed 406, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.html - lines changed 150, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.ra - lines changed 103, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliSeq.html - lines changed 150, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliSeq.ra - lines changed 103, context: html, text, full: html, text
- Changed RepliSeq to Repli-chip. Redmine #6627.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeFsuRepliChip.ra - lines changed 1158, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeFsuRepliSeq.ra - lines changed 1158, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeFsuRepliChip.html - lines changed 149, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeFsuRepliChip.ra - lines changed 238, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeFsuRepliSeq.html - lines changed 149, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeFsuRepliSeq.ra - lines changed 238, context: html, text, full: html, text
- Fixed meta-data that was missed in the renaming . Redmine #6627.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeFsuRepliChip.ra - lines changed 219, context: html, text, full: html, text
- Added UCSC accessions to the track and ready for approval. Redmine #6626.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeFsuRepliChip.ra - lines changed 41, context: html, text, full: html, text
- Added release 1 notes. Redmine #6626.
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeFsuRepliChip.release1.notes - lines changed 92, context: html, text, full: html, text
- Fixes for Redmine #6626
1. Description section: In the first sentence, changed "is" to "was".
2. Description section: In the third sentence, "loess-smoothed" added hyphen
3. Description section: In the third sentence, "individual" fixed spelling
4. Methods section, first paragraph: In the Hiratani reference, removed "i"
5. Methods section, first paragraph: Added month to reference to specify with Ryba paper
6. Methods section, Extraction protocol subsection: Lower cased the protocol
7. Methods section, Extraction protocol subsection: In the second sentence, removed "briefly"
8. Methods section, Extraction protocol subsection: changed "are" to "were".
11. Methods section, Hybridization protocol subsection: fixed link
12. Methods section, Hybridization protocol subsection: Change "The hybridization step used the standard NimbleGen protocol."
13. Methods section, Hybridization protocol subsection: In the second sentence, removed "briefly"
14. Methods section, Hybridization protocol subsection: In the second sentence, added hyphen after "Cy3" and a hyphen between "Cy5" and "labeled".
15. Methods section, Hybridization protocol subsection: In the second sentence,replaced "u" with "μ" for micrograms.
16. Methods section, Hybridization protocol subsection: In the second sentence, added hyphen "evenly-spaced"
18. Methods section, Scan protocol subsection: Removed special chacter
19. Methods section, Scan protocol subsection: made "pe" to "per".
20. Methods section, Scan protocol subsection: Fixed link.
21. Methods section, Data processing subsection: In the second sentence, added hyphen after "early" and "late-replicating"
22. Methods section, Data processing subsection: At the end of the second sentence, add "then" before "averaged"
23. Methods section, Data processing subsection: In the last sentence, removed - after 300
24. Credits section: Fixed email link
- src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.html - lines changed 14, context: html, text, full: html, text
- Fixes for Redmine #6626
9. Methods section, Extraction protocol subsection: Merged second and third sentence.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.html - lines changed 1, context: html, text, full: html, text
- Fixes for redmine #6626
11b. Fixed link to not be relative link
20b. Fixed link to not be relative link
24b. Removed < in email link
28. Track Height set to 32
- src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.html - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.ra - lines changed 1, context: html, text, full: html, text
- 30. Removed dateUnrestricted for: H9ES, H7-ESC, GM06990, BG02ES. Redmine #6626.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeFsuRepliChip.ra - lines changed 13, context: html, text, full: html, text
- Removed G1E H3k4me1 experiment due to peaks being suspect. Moved experiment to release 2. Redmine #111.
- src/hg/makeDb/doc/encodeDccMm9/wgEncodePsuHistone.release1.notes - lines changed 26, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra - lines changed 22, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.release2.ra - lines changed 52, context: html, text, full: html, text
- Moved approved changes from beta to public. Redmine #7641.
- src/hg/makeDb/trackDb/cv/public/cv.ra - lines changed 355, context: html, text, full: html, text
- Fixed spelling of Provisional. Also fixed biochain links.
- src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 123, context: html, text, full: html, text
- Fixed for Redmine #111
3. Description Section, third paragraph changed "are" to "is"
6. Capatalized bowtie
7. Removed comman after "Since"
8. Added "the" to downloads page link
11. Fixed spacing issue in references links, by moving "</a>." to same line as article title
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.html - lines changed 24, context: html, text, full: html, text
- Added a to make sentence readable. Redmine #111.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.html - lines changed 1, context: html, text, full: html, text
- Moved the out of the link for the downloads page. Redmine #111.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.html - lines changed 2, context: html, text, full: html, text
- Added first name to reference of Hardison in Contact section. Redmine #111.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.html - lines changed 1, context: html, text, full: html, text
- Fixed hash bang.
- python/programs/cvValidate/cvValidate - lines changed 1, context: html, text, full: html, text
- Added readtype. Redmine #4469.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra - lines changed 217, context: html, text, full: html, text
- Added readTypes for LICR RNA-seq data set.
- src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 5, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrRnaSeq.ra - lines changed 134, context: html, text, full: html, text
- Fixed pairing of controls. Redmine #4486.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 261, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.ra - lines changed 60, context: html, text, full: html, text
- Added missign control for GM08174. Redmine #4486.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 65, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.ra - lines changed 8, context: html, text, full: html, text
- Fixed naming of control for experiment from UCD to STD. Redmine #4486.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 27, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.ra - lines changed 6, context: html, text, full: html, text
- Fixed ENCODE freeze date.
- src/hg/utils/automation/Encode.pm - lines changed 4, context: html, text, full: html, text
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