Uploads by Hiram
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This special page shows all uploaded files.
| Date | Name | Thumbnail | Size | Description | Versions |
|---|---|---|---|---|---|
| 17:43, 19 March 2015 | MatrixSummary pl.txt (file) |  |
6 KB | used in lastz tuning procedure, examines output of the four lastz_D outputs to survey the differences | 1 |
| 17:17, 19 March 2015 | Create scores file control.txt (file) | |
653 bytes | Parameters from Bob Harris for lastz tuning procedure | 1 |
| 17:14, 19 March 2015 | Expand scores file py.txt (file) | |
4 KB | Script created by Bob Harris for lastz tuning operations | 1 |
| 17:10, 19 March 2015 | AdjustSizes pl.txt (file) | |
3 KB | chrom.sizes files are now expected to exist as created by selectedFasta.sh | 2 |
| 17:09, 19 March 2015 | SelectedFasta sh.txt (file) | |
2 KB | generalize the chrom.size creation and noMask option on fasta creation | 2 |
| 23:34, 18 March 2015 | TopAll sh.txt (file) | |
2 KB | script used in lastz tuning procedure to run lastz_D on different sets of DNA sequences from query and target | 1 |
| 23:18, 18 March 2015 | MafScoreSizeScan pl.txt (file) | |
2 KB | script used to scan a MAF file to extract scores, sizes, and coverage statistics of each alignment block. Used in lastz tuning procedures. | 1 |
| 20:59, 4 February 2014 | BME230 Winter 2014.ppt (file) |  |
13.79 MB | Hiram's presentation to BME230 Winter 2014 11 February - brief browser usage introduction, assembly hub demonstration, table browser intersection, plus information on source code but not part of the discussion) | 1 |
| 22:36, 6 June 2013 | AssemblyHubs BoG 2013.pptx (file) | |
2.72 MB | Assembly Hubs, Biology of Genomes meeting 2013 CSHL | 1 |
| 22:35, 6 June 2013 | AssemblyHubs BoG 2013.pdf (file) |  |
3.06 MB | Assembly Hubs, Biology of Genomes meeting 2013 CSHL | 1 |
| 05:43, 13 March 2013 | SameSpeciesChainNet.sh.txt (file) | |
5 KB | Same species lift over, step 2 of 2, chain/net the blat psl results together into the result file | 1 |
| 05:04, 13 March 2013 | BlatJob.csh.txt (file) | |
2 KB | script to use for the same species lift over procedure run.blat/ step 1 | 1 |
| 04:57, 13 March 2013 | SameSpeciesBlatSetup.sh.txt (file) | |
6 KB | First step in the same species lift over procedure, set up for blat run, adding 11.ooc file construction for blat | 2 |
| 02:56, 29 June 2012 | FireCracker10KElevationProfile.png (file) |  |
6 KB | Elevation profile for the Santa Cruz FireCracker 10K run, July 4th. Corrected the GPS readings with Google Earth information and known ground truth. | 2 |
| 16:44, 27 April 2012 | DanRer7.ncbiIncidentDb.bb (file) | |
168 KB | gwUploadFile upload | 27 |
| 16:43, 27 April 2012 | Mm9.ncbiIncidentDb.bb (file) | |
136 KB | gwUploadFile upload | 80 |
| 16:43, 27 April 2012 | Hg19.ncbiIncidentDb.bb (file) | |
179 KB | gwUploadFile upload | 67 |
| 21:27, 25 January 2012 | BME230 Winter 2012.ppt (file) | |
7.31 MB | Hiram's presentation to BME230 Winter 2012 26 January 2012 - brief browser usage introduction, table browser intersection, plus information on source code but not part of the discussion | 1 |
| 21:51, 5 October 2011 | XLDB 2011.pptx (file) | |
1.23 MB | bigBed/bigWig 5 minute presentation at XLDB conference, Stanford, 18 October 2011. | 2 |
| 18:48, 24 August 2011 | Sol GCBias GeneCats 2011-08-24.pdf (file) | |
1.4 MB | Sol Katzman presentation, genecats 24 Aug 2011 | 1 |
| 16:43, 24 June 2011 | ExtractRepeats.txt (file) | |
2 KB | Small perl script used to extract lineage specific repeats from RepeatMasker .out files | 1 |
| 20:14, 22 March 2011 | 29mammalsConstrainedElements pi lods.bw (file) | |
61.15 MB | gwUploadFile upload | 1 |
| 20:13, 22 March 2011 | 29mammalsConstrainedElements pi branchLength.bw (file) | |
61.3 MB | gwUploadFile upload | 1 |
| 20:13, 22 March 2011 | 29mammalsConstrainedElements omega lods.bw (file) | |
54.74 MB | gwUploadFile upload | 1 |
| 20:13, 22 March 2011 | 29mammalsConstrainedElements omega branchLength.bw (file) | |
54.38 MB | gwUploadFile upload | 1 |
| 20:43, 21 March 2011 | 29mammalsConstraintStructure.bw (file) | |
219 KB | test upload | 1 |
| 20:42, 21 March 2011 | 29mammalsMotifInstances.bb (file) | |
38.25 MB | test upload | 1 |
| 20:41, 21 March 2011 | 29mammalsExaptedElements.bb (file) | |
3.51 MB | test upload | 1 |
| 20:36, 21 March 2011 | 29mammals2xHARs.bb (file) | |
45 KB | test upload | 1 |
| 20:33, 21 March 2011 | 29mammals2xPARs.bb (file) | |
45 KB | test upload | 1 |
| 20:31, 21 March 2011 | 29mammalsNovelExons.bb (file) | |
411 KB | test upload | 1 |
| 23:44, 25 January 2011 | ConstructLiftFile pl.txt (file) | |
1 KB | Given a partition list from partitionSequence.pl and a chrom.sizes file, this perl script will construct a lift file to be used to lift psl query and target results from those partitions after a lastz alignment. | 1 |
| 17:28, 6 January 2011 | BME230 Winter 2011.ppt (file) | |
6.25 MB | Hiram Clawson, BME 230 lecture, 06 January 2011, introduction to the genome browser and programming with the kent source tree. | 1 |
| 18:04, 15 September 2010 | Knetfile hooks.0.1.7.patch (file) | |
13 KB | Patch to samtools-0.1.7 to enable UCSC network functions and caching for remote BAM file access | 1 |
| 18:03, 15 September 2010 | Knetfile hooks.0.1.8.patch (file) | |
16 KB | Patch to samtools-0.1.8 to enable UCSC network functions and caching for remote BAM file access | 1 |
| 20:57, 16 June 2010 | Ce6Ws190AltSpliceCustomTrack.txt (file) | |
172 bytes | the custom track reference track line for ce6/WS190 alternative splice track | 1 |
| 20:55, 16 June 2010 | Ce6.altSplice.bb (file) | |
213 KB | Alternate splice sites lifted from WS170 track to WS190 coordinates from IntronWS120 file: altsplice.EX.html) | 1 |
| 20:48, 16 June 2010 | Ce2Ws120AltSpliceCustomTrack.txt (file) | |
172 bytes | adding db=ce2 definition | 3 |
| 20:47, 16 June 2010 | Ce4Ws140AltSpliceCustomTrack.txt (file) | |
194 bytes | adding db=ce4 definition | 2 |
| 20:44, 16 June 2010 | Ce4.altSplice.bb (file) | |
213 KB | Alternate splice sites lifted from WS120 track to WS170 coordinates from IntronWS120 file: altsplice.EX.html) | 1 |
| 20:39, 16 June 2010 | Ce2.altSplice.bb (file) | |
212 KB | Alternate splice sites from IntronWS120 file: altsplice.EX.html | 4 |
| 18:31, 19 March 2010 | Hg17.customText.UCSC GGM SpecificCGIs.txt (file) | |
257 bytes | customText track definition for hg17 custom track: CGIs (specific) - Bona fide CpG islands, predicted to exhibit a combined epigenetic score above 0.67 | 1 |
| 18:30, 19 March 2010 | Hg17.customText.UCSC GGM SensitiveCGIs.txt (file) | |
296 bytes | customText track definition for hg17 custom track: CGIs (sensitive) - Bona fide CpG islands, predicted to exhibit a combined epigenetic score above 0.33 | 1 |
| 18:29, 19 March 2010 | Hg17.customText.UCSC GGM CombinedEpigeneticScore.txt (file) | |
272 bytes | customText track definition for hg17 custom track: Epigenetic score - Combined epigenetic score (high scores correspond to bona fide CpG islands) | 1 |
| 18:28, 19 March 2010 | Hg17.customText.UCSC GGM BalancedCGIs.txt (file) | |
257 bytes | customText track definition for hg17 custom track: CGIs (balanced) - Bona fide CpG islands, predicted to exhibit a combined epigenetic score above 0.5 | 1 |
| 18:27, 19 March 2010 | Hg17.customText.UCSC GGM All.txt (file) | |
1 KB | customText track definition for all five data sets UCSC GGM CpGs | 1 |
| 18:25, 19 March 2010 | Hg17.UCSC GGM SpecificCGIs.bb (file) | |
178 KB | bigBed data for hg17 custom track: CGIs (specific) - Bona fide CpG islands, predicted to exhibit a combined epigenetic score above 0.67 | 1 |
| 18:23, 19 March 2010 | Hg17.UCSC GGM SensitiveCGIs.bb (file) | |
686 KB | bigBed data for hg17 custom track: CGIs (sensitive) - Bona fide CpG islands, predicted to exhibit a combined epigenetic score above 0.33 | 1 |
| 18:22, 19 March 2010 | Hg17.UCSC GGM OptimizedScore.bb (file) | |
1.99 MB | bigBed data for hg17 custom track: Optimized score - Optimized score (high scores correspond to bona fide CpG islands | 1 |
| 18:21, 19 March 2010 | Hg17.UCSC GGM CombinedEpigeneticScore.bb (file) | |
2.02 MB | bigBed data for hg17 custom track: Epigenetic score - Combined epigenetic score (high scores correspond to bona fide CpG islands) | 1 |
