Search results
From OpenWetWare
Jump to navigationJump to search
- PersonalGenomes@Home (section Alignment with Bowtie)typically about 2.2 GB for the human genome. See also: Bowtie paper in Genome Biology. We have used bowtie with its default settings to align the PGP2 data from...14 KB (11 words) - 14:03, 1 July 2009
- existing genomic sequence SOAP suite of programs, no de novo assembly (yet). Bowtie "fast and memory efficient" The most complete list to date is @seqanswers...4 KB (436 words) - 15:34, 12 February 2010
- authors with version 1.3.0) bowtie (works with 0.12.7) Also completes running example with Python 2.7.1rc1, numpy-1.5.1 and bowtie 0.12.7 on in-house data...12 KB (1,677 words) - 02:50, 30 September 2014
- on protein family covariation Humann2 First maps reads to reference db (bowtie), then homology search with higher sensitivity Two steps for computational...824 bytes (110 words) - 13:06, 7 August 2017
- Oligonucleotide Analysis Package. MAQ - Mapping and Assembly with Qualities. Bowtie - Bowtie. An ultrafast, memory-efficient short read aligner. BWA - Burrows-Wheeler...5 KB (461 words) - 13:17, 20 June 2012
- Oligonucleotide Analysis Package. MAQ - Mapping and Assembly with Qualities. Bowtie - Bowtie. An ultrafast, memory-efficient short read aligner. BWA - Burrows-Wheeler...8 KB (647 words) - 17:46, 5 June 2012
- tree) as a constraint in RAXML Martin: used phyML for whole genome tree Try bowtie? only for human... JE: ask Sanderson's group Any reason not to use a guide...2 KB (285 words) - 14:53, 17 August 2017
- suffix arrays Previously used for aligning short reads to genomes (BWA, Bowtie) Recently applied to assembly (extension of SGA assembler, really sped it...2 KB (309 words) - 10:39, 7 August 2017
- is available on the MAQ page. Bowtie - The Burge Lab is currently analyzing the quality of reads mapped using Bowtie. Bowtie is believed to be MUCH faster...16 KB (2,406 words) - 12:14, 13 January 2011
- users to get their data faster. Release Notes 1.0.2 (08/19/2013) Switch from Bowtie to BWA for default alignments for generating SAM files. The BWA version...13 KB (1,993 words) - 08:21, 14 December 2022
- Wikiomics:WinterSchool day2 (section bowtie2)your PATH following programs: bowtie2 and bowtie2-align bowtie2-inspect bowtie2-build samtools #run tophat2 (with bowtie2) using also gene annotation:...25 KB (4,166 words) - 10:56, 11 September 2014
- Raw sequences are pre-processed and aligned using various options (BWA or Bowtie). The GeZnome Analysis Took Kit (GATK) and SAMtools are used to call variants...9 KB (431 words) - 13:34, 29 October 2018
- muscle/3.8.31(default) tabix/0.2.6 bowtie/2.0.0b3(default) freec/5.7(default) novoalign/2.08.03(default) tmhmm/2.0c(default) bowtie2/2.0.0-beta5 gasv/2012.10.12...9 KB (1,186 words) - 11:07, 14 December 2022
- reference_seq with bowtie2. First we need to create an index of the reference sequence: $ bowtie2-build reference_seq.fa.gz bowtie_reference_seq Let's...33 KB (4,704 words) - 07:18, 27 September 2017
- bwa_map_050 and another 30 jobs bowtie_map_001 to bowtie_map_030. We want to remove all our still running or submitted and waiting bowtie_map jobs, but do not touch...44 KB (7,298 words) - 08:55, 27 November 2013
- multiple times to the mouse genome (mm9) are shown. Reads were aligned with Bowtie. NuGen samples show an increase in non-aligned reads at low input amounts...9 KB (288 words) - 17:49, 19 June 2012
- /home/heather/trunk/tmp <br /> BowtieToBedFormat: [mkdir] Created dir: /home/heather/trunk/tmp [jar] Building jar: /home/heather/trunk/jars/fp4/BowtieToBedFormat.jar [delete]...3 KB (0 words) - 17:20, 26 September 2017
- /home/oeil/trunk/tmp<br/> BowtieToBedFormat:<br/> [mkdir] Created dir: /home/oeil/trunk/tmp<br/> [jar] Building jar: /home/oeil/trunk/jars/fp4/BowtieToBedFormat.jar<br/>...3 KB (0 words) - 17:20, 26 September 2017
- /home/heather/trunk/tmp BowtieToBedFormat: [mkdir] Created dir: /home/heather/trunk/tmp [jar] Building jar: /home/heather/trunk/jars/conversion_util/BowtieToBedFormat...15 KB (0 words) - 17:32, 26 September 2017
- 2009;10(3):R25. DOI:10.1186/gb-2009-10-3-r25 | PubMed ID:19261174 | HubMed [bowtie] Trapnell C, Pachter L, and Salzberg SL. TopHat: discovering splice junctions...7 KB (1,427 words) - 16:31, 4 April 2012
