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(desc) Avg read len fastq.awk . . 561 bytes . . Yhernand . . 21:33, 7 February 2013 (Awk script to read a FASTQ file and count up read lengths. Produces output suitable for creating a histogram in R, for example. Also outputs the number of reads read)
(desc) Deltav mismatch guide matrix.png . . 124,612 bytes . . Yhernand . . 17:21, 9 January 2013
(desc) Function table.png . . 141,067 bytes . . Yhernand . . 01:43, 9 January 2013
(desc) Deltav mismatch guide matrix.svg . . 51,707 bytes . . Yhernand . . 22:51, 7 January 2013 (Draft of \Delta V guide matrix figure showing regions within matrix.)
(desc) CompletedApplication.pdf . . 294,451 bytes . . Jloving . . 17:33, 16 November 2012
(desc) KB1 unpaired boxplot qual mid50.svg . . 3,529,977 bytes . . Yhernand . . 21:59, 16 October 2012 (Boxplot showing the quality statistics of the reads in the KB1 (unpaired/single) genome. This boxplot shows the middle 50 in the box portion.)
(desc) KB1 unpaired boxplot qual mid90.svg . . 3,526,990 bytes . . Yhernand . . 21:58, 16 October 2012 (Boxplot showing the quality statistics of the reads in the KB1 (unpaired/single) genome. This boxplot shows the middle 50 in the box portion.)
(desc) OFmaskedAfterRedundancyhg19277.jpg . . 3,181 bytes . . Gbenson . . 18:10, 9 October 2012
(desc) OFmaskedNoRedundancyHG19277.jpg . . 3,083 bytes . . Gbenson . . 18:07, 9 October 2012 (HG19 2 7 7 before any redundancy elimination)
(desc) HG19 reference after IFmasked le 20 filter TR intervals with only one TR . . 21,411 bytes . . Gbenson . . 19:48, 2 October 2012
(desc) HG19 reference TR intervals with more than one TR.pdf . . 14,995,164 bytes . . Gbenson . . 19:15, 2 October 2012
(desc) HG19 reference TR intervals with only one TR and pattern size ge 7.pdf . . 21,433 bytes . . Gbenson . . 18:58, 2 October 2012
(desc) HG19 reference TR intervals with only one TR and pattern size ge 7 code . . 21,433 bytes . . Gbenson . . 18:52, 2 October 2012
(desc) HG19 reference TR intervals with only one TR and pattern size ge 7 . . 21,433 bytes . . Gbenson . . 18:50, 2 October 2012
(desc) Example.jpg . . 21,433 bytes . . Gbenson . . 18:50, 2 October 2012
(desc) HG19 reference TR intervals with only one TR.pdf . . 20,956 bytes . . Gbenson . . 18:39, 2 October 2012
(desc) Array Length Distribution 2 7 7 avg score ge 1.3 finer resolution.jpg . . 4,899 bytes . . Gbenson . . 19:55, 25 September 2012
(desc) Array Length Distribution 2 7 7 original finer resolution.jpg . . 4,690 bytes . . Gbenson . . 19:55, 25 September 2012
(desc) Array Length Distribution 2 7 7 original.jpg . . 3,784 bytes . . Gbenson . . 19:46, 25 September 2012
(desc) Array Length Distribution 2 7 7 avg score ge 1.3.jpg . . 3,943 bytes . . Gbenson . . 19:43, 25 September 2012
(desc) Avg Score vs Array Length 2 7 7 avg score ge 1.3.jpg . . 10,434 bytes . . Gbenson . . 19:38, 25 September 2012
(desc) Avg Score Distribution 2 7 7 avg score ge 1.3.jpg . . 3,879 bytes . . Gbenson . . 19:34, 25 September 2012
(desc) Avg Score Distribution 2 7 7 original.jpg . . 3,868 bytes . . Gbenson . . 19:26, 25 September 2012
(desc) Avg Score vs Array Length 277 original.jpg . . 22,328 bytes . . Gbenson . . 19:15, 25 September 2012
(desc) Avg Score Distribution.jpg . . 3,695 bytes . . Gbenson . . 19:10, 25 September 2012
(desc) Watson quality boxplot mid90.svg . . 2,021,971 bytes . . Yhernand . . 22:54, 19 September 2012 (Boxplot showing the quality statistics of the reads in the Watson genome. The X-axis shows the Position, while the Y-axis represents the quality score. Boxplots are given a different color for each position to help distinguish them. This boxplot shows the)
(desc) Watson quality boxplot mid80.svg . . 2,021,852 bytes . . Yhernand . . 22:54, 19 September 2012 (Boxplot showing the quality statistics of the reads in the Watson genome. The X-axis shows the Position, while the Y-axis represents the quality score. Boxplots are given a different color for each position to help distinguish them. This boxplot shows the)
(desc) Hitspq watson full aug21.svg . . 260,931 bytes . . Yhernand . . 22:26, 19 September 2012
(desc) Querieshr watson full aug21.svg . . 549,840 bytes . . Yhernand . . 22:26, 19 September 2012
(desc) Watson quality boxplot.svg . . 1,984,642 bytes . . Yhernand . . 16:39, 15 September 2012 (Boxplot showing the quality statistics of the reads in the Watson genome. The X-axis shows the Position, while the Y-axis represents the quality score. Boxplots are given a different color for each position to help distinguish them.)
(desc) Querieshr watson full aug21 nidx.svg . . 160,901 bytes . . Yhernand . . 17:13, 12 September 2012 (Histogram showing the distribution of times each read, NOT found in an index file, was hit. This is only counting the number of times a read showed up as a hit for a query (reference), and not HSPs.)
(desc) Querieshr watson full aug21 index.svg . . 622,244 bytes . . Yhernand . . 17:12, 12 September 2012 (Histogram showing the distribution of times each read, found in an index file, was hit. This is only counting the number of times a read showed up as a hit for a query (reference), and not HSPs.)
(desc) Timesrh watson full aug21.png . . 19,126 bytes . . Yhernand . . 17:46, 5 September 2012
(desc) Hitspq watson full aug21.png . . 18,441 bytes . . Yhernand . . 17:40, 5 September 2012 (Histogram showing the distribution of hits for each query. This is only counting hits (reads) for each query (reference), and not HSPs. Limited to 30 hits and a frequency of 900.)
(desc) Avg qual per position.png . . 56,180 bytes . . Yhernand . . 20:50, 30 August 2012 (Average quality per base for the entire Watson genome data set. Average is taken using the total count of quality scores per base, since not all sequences are of the same length.)
(desc) VennDiagram.jpg . . 1,436,751 bytes . . Jloving . . 18:38, 24 August 2012
(desc) Blast hit read 1773403177.txt . . 9,286 bytes . . Yhernand . . 16:51, 24 August 2012 (BLAST hit summary for read 'gnl|ti|1773403177 name:EIW8CDE01B96UF' using reference 162407910 as the query sequence. There are 9 HSPs found using this read.)
(desc) Blast hit frac found.png . . 17,744 bytes . . Yhernand . . 19:24, 16 August 2012 (Bar plot of the fraction of BLAST hit found in the index files with a given length. Supposing if 1000 reads of length 220 were found in total by BLAST, but only 400 of those were in reads that were found in the index file, then the height of the bar would)
(desc) Blast hit length hist.png . . 19,899 bytes . . Yhernand . . 19:54, 15 August 2012 (A histogram of lengths of subject strings in BLAST hits from a search of unclustered repeat sequences against reads in the Watson genome. All subject string lengths in each BLAST hit are binned in bins of size 10 and counted to produce this histogram.)
(desc) ParseXML sample code for iphone class wiki . . 8,659 bytes . . Gbenson . . 15:30, 17 October 2010
(desc) Instructions for registering as apple developer and putting apps on iPhone.txt . . 3,455 bytes . . Gbenson . . 21:09, 23 June 2010
(desc) MKMapView example.txt . . 8,128 bytes . . Gbenson . . 20:22, 23 June 2010
(desc) UIWebview example code.txt . . 4,692 bytes . . Gbenson . . 20:09, 23 June 2010
(desc) Saving Data by Archiving.txt . . 3,361 bytes . . Gbenson . . 20:01, 17 June 2010
(desc) Saving Data example.txt . . 3,182 bytes . . Gbenson . . 20:11, 16 June 2010
(desc) URL Connection example.txt . . 4,612 bytes . . Gbenson . . 20:10, 15 June 2010
(desc) Singleton class.txt . . 2,071 bytes . . Gbenson . . 17:02, 15 June 2010
(desc) Mygarden.txt . . 996 bytes . . Gbenson . . 13:23, 15 June 2010
(desc) Botanical.plist . . 1,448 bytes . . Ygelfand . . 18:47, 14 June 2010
(desc) Botanical.txt . . 1,395 bytes . . Gbenson . . 16:12, 14 June 2010

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Protein Engineering